Contaminants of Concern in Water Bodies of Puerto Rico
Carmen Hernández
Fall 2019
Honors Thesis
Summa Cum Laude
Department of Soil and Water
College of Agricultural and Life Sciences
University of Florida
University Faculty: Dr. Bala Rathinasabapathi
Abstract:
Contaminants of concern are chemical, biological, or radioactive materials found
in effluents, sediments, or other substances generated by natural phenomena or human
activities. Indicator parameters are focal contaminants of concern that are characteristic
of water quality deterioration. The purpose of this research project is to generate a report
on water quality standards and pollution mitigation by identifying contaminants of concern
and indicator parameters for wastewater effluents. This information could establish a
scheme of steps to understand wastewater effluents and define future steps necessary
to treat the water to reuse it beneficially.
The specific objectives of this research are:
• Evaluate the Puerto Rico Water Quality Assessment (2018)
• Identify the contaminants of concern and indicator parameters for specific designated
uses
• Categorize contaminants of concern by the bulk of water quality, inorganic, organic,
or metal constituents
• Identify contaminants of concern and indicator parameters for domestic wastewater
treatment plants and confined animal feeding operations
• Adverse impacts on fauna, aquatic life, and humans
• Recommendations to prevent and treat contaminants at the source of pollution
• Provide educational information to the general public in a concise and useful manner
Table of Contents
List of Tables and Figures…………………………………………………………………...…1
1. Introduction………………………………………………………………………………..….2
2. Methods…………………………………………………………………………………........3
2.1.0 Water Resources in Puerto Rico……………………………………...……....3
2.1.1 Surface Water……………………………………………………..........3
2.1.2 Groundwater………………………………………………………….….4
2.1.3 Water Uses………………………………………………………………5
2.2.0 Data Collection…………………………………………………………………..6
3. Results……………………………………………………………………………………...…7
3.1.0 Contaminants of Concern in Water Bodies…………………………………....7
3.1.1 River and Streams………………………………………………….......10
3.1.2 Lakes (reservoirs)…………………………………………………........11
3.1.3 San Juan Bay Estuary……………………………………………….…13
4. Discussion…………………………………………………………………………………..14
4.1.0 Sources of Pollution…………………………………………………………....15
4.1.1 Domestic Wastewater Treatment Plants………………………….…16
4.1.2 Confined Animal Feeding Operations………………………………..19
5. Conclusion……………………………………………………………………………….….21
6. References……………………………………………………………………………….…22
1
List of Figures and Tables
Figure 1. Surface Water Resources………………………………………………...……………4
Figure 2. Groundwater Resources…………………………………………………………..……5
Figure 3a-c. Proportions of Water Use in Puerto Rico from Surface and Groundwater………..6
Table 1. Steps Descriptions………………………………………………………………………6
Table 2. Water Bodies…………………………………………………………………………….7
Table 3. Pollution Source Groups………………………………………………………………..7
Table 4. Water Quality Standards Parameter Limits …………..…….………………………..8
Table 5. Water Quality Standards Assessment for Rivers and Streams……………………10
Table 6. River and Streams Contaminants of concern…………………………………….....11
Table 7. Water Quality Standards Assessment for Lakes (reservoirs)…………………..….12 Table 8. Lakes (Reservoirs) Contaminants of concern………………………………………..12
Table 9. Water Quality Standards Assessment for San Juan Bay Estuary…………………13
Table 10. San Juan Bay Estuary Contaminants of concern……………………………………14
Table 11. Potential Sources of Pollution………………………………………………………….15
Table 12. Wastewater Treatment Plants Contaminants of Concern…………………………..18
Table 13. Confined Animal Feeding Operations Contaminants of Concern……………….….20
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1. Introduction
Sustainability is defined by the United States National Environmental Policy Act of 1969 (NEPA)
as “create and maintain conditions, under which humans and nature can exist in productive harmony,
that permit fulfilling the social, economic, and other requirements of present and future generations”
(Sustainability Primer, 2019). A sustainable approach consists of three pillars: environmental, social,
and economic. Identifying contaminants of concern, mitigating water pollution, implementing best
management practices, and reusing water could have a positive effect on the three components of the
sustainability approach. First, the environmental pillar covers the identification of the contaminants
present in rivers, streams, lakes, and the San Juan Bay Estuary, and possible solutions to mitigate
pollution inputs in these water bodies. Next, the participation of the social component is to protect and
improve human health through the education of the general public on identifying contaminants of
concern in surface and groundwater resources, wastewater effluents and constituents from potential
pollutant sources, and recommendations to mitigate the pollution. Finally, the economic pillar involves
reducing the cost and amount of potable water used in industries of potential pollution sources when
treating and reusing their wastewater effluents.
First, we will evaluate and discuss Puerto Rico’s water quality standards assessment for rivers,
streams, lakes (reservoirs), and the San Juan Bay Estuary, by body size (miles), and attained category.
Next, identify contaminants of concern and indicator parameters for primary contact recreation,
secondary contact recreation, and raw source of drinking water designated uses. Categorize
contaminants of concern by the bulk of water quality, inorganic, organic, or metal constituents. Finally,
characterize pollutants in domestic wastewater plants and confined animal feeding operations.
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2. Methods
2.1.0 Water Resources in Puerto Rico
It is fundamental to understand water resources in Puerto Rico to recognize the potential of
reusing wastewater. Approximately 88% of the water resources in Puerto Rico comes from surface
water, and the other 12% comes from groundwater (Water Use Data, 2015). In Puerto Rico, 60% of
domestic wastewater comes from septic tanks. These effluents are discharged directly into water
bodies. The other 40% of domestic wastewater comes from municipal discharges. A study by the
Departamento de Recursos Naturales y Ambientales (2005), determined that municipal discharges
generate approximately 223 million of gallons per day (MGD) of domestic wastewater, of which 149
MGD (67%) receive primary treatment, 63 MGD (28%) secondary, and 11 MGD (5%) tertiary. Domestic
wastewater treatment involves a combination of physical, chemical, and biological processes to remove
solids, organic matter, bacteria, and nutrients dissolved or suspended in its effluents (See 4.1.1,
Domestic Wastewater Treatment Plants). After treatment, these effluents are reintroduced to the ocean
(primary treatment), as well as streams, rivers, reservoirs, and estuaries (Inventario de Recursos,
2005). This vast quantity of water constitutes a significant resource with the potential for reuse for
diverse activities, including agricultural irrigation, and aquifer recharge.
2.1.1 Surface Water
Surface waters represent the most critical water resource in Puerto Rico. The physiography of
the Island includes 224 rivers and 553 streams, formed by the combined effects of climate and
geology (Morris et al., 2008). The abundance of rain over these water bodies contribute to a
significant water flow for most of the year (Fig.1). Even though there are no natural lakes in Puerto
Rico, there are 37 water reservoirs (dams). Water dams are the principal source of water for
consumption, industrial production, and agriculture operations (Morris et al., 2008).
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Fig. 1 – Surface Water Resources – Image reproduce from the National Map Viewer website.
2.1.2 Groundwater
Puerto Rico has a diversity of geological formations that function as aquifers. These geological
formations are grouped into three types of fundamental geological formations: Alluvial deposits,
limestone (karst), and igneous rock (Fig. 2). An aquifer is a geological formation saturated with water.
An aquifer volume and permeability are plentiful to sustain the extraction of freshwater (Morris et al.,
2008). The North Coast Aquifers comprise an area of 2341 Km2 and consist of limestone rock (Karst)
and alluvial formations in river valleys (Morris et al., 2008). The alluvial aquifers in the floodplains are
composed of unconsolidated sand formations and permeable gravels deposited by ancient rivers. Thus,
alluvial aquifers have the highest groundwater recharge in Puerto Rico (Morris et al, 2008). The aquifers
in the inner valleys generally consist of alluvial deposits, fractured rock, and slight limestone (karst)
formations. These aquifers do not discharge into the sea. Therefore, they are not subject to saltwater
intrusion. However, the presence of iron and manganese have caused water quality deterioration in
some areas (Morris et al., 2008).
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Fig. 2 – Groundwater Resources – Image reproduced from the US. Geological Survey website.
2.1.3 Water Uses
According to data collected by the United States Geological Survey (2015), Puerto Rico
extracted 577 million gallons per day (MGD) of fresh water to meet their social and economic needs.
Of this total, 510 MGD (88%) came from surface water and 67 MGD (12%) from groundwater resources
(Fig. 3a). Domestic supply is the primary freshwater consumer in Puerto Rico. It used 339 MGD (59%)
of freshwater, 338 MGD (66%) are allocated to surface waters (Fig. 3b) and approximately 1 MGD
(approximate 1%) to groundwater resources (Fig. 3c). The next top freshwater consumer is agriculture.
It utilized 218 MGD (38%) of freshwater, 161 MGD (32%) are allocated to surface water (Fig. 3b), and
57 MGD (85%) to groundwater resources (Fig. 3c). The least freshwater consumer is industrial use, it
extracted 20 MGD (3%) of the freshwater,11 MGD (2%) are allocated to surface water (Fig. 3b) and 9
MGD (14%) to groundwater resources (Fig. 3c) (Water Use Data, 2015).
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Fig. 3a Fig. 3b Fig. 3c
Fig. 3a-c – Proportions of Water Use in Puerto Rico from Surface and Groundwater
2.2.0 Data Collection
Table 1 – Steps Descriptions
Steps Description
1
• Identify information resources to determine contaminants of concern in water bodies of Puerto Rico, which includes but not limited to:
o Puerto Rico Water Quality Assessment Report (2018).
o Puerto Rico Water Quality Standards Regulation (2019).
o Integrated Reporting Guidance under CWA Sections 303(d), 305(b), and 314(2019).
o NPDES Permit Writers' Manual (2010).
o Peer-review publications and scientific journal articles
2
• Evaluate and discuss Puerto Rico Water Quality Standards Assessment for rivers, streams, lakes (reservoirs), and the San Juan Bay Estuary by body size (miles) and attained category.
• Identify contaminants of concern and indicator parameters for primary contact recreation, secondary contact recreation, and raw source of drinking water designated uses.
o Contaminants of concern are chemical, biological, or radioactive materials found in effluents, sediments, or other substances generated by natural phenomena or human activities.
o Indicator parameters are focal contaminants of concern that are characteristic of water quality deterioration.
• Categorize contaminants of concern by:
o The Bulk of water quality
o Inorganic, organic, or metals constituents
3
• Identify the contaminants of concern and indicator parameters for domestic wastewater treatment plants and confined animal feeding operations.
• Categorize contaminants of concern by:
o The Bulk of water quality
o Inorganic, organic, or metals constituents
• Possible impacts on fauna, aquatic life, and humans
• Recommendations to mitigate water pollution
12%
88%
GROUNDWATER
SURFACE WATER
66%2%
32%
SURFACE WATER
DOMESTIC SUPPLY
INDUSTRIAL
AGRICULTURE
1%14%
85%
GROUNDWATER
DOMESTIC SUPPLY
INDUSTRIAL
AGRICULTURE
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Table 2 – Water Bodies
Waterbody Type
River and Streams
Lakes (Reservoirs)
San Juan Bay Estuary
Table 3 – Pollution Source Groups
Source Group Source
Agriculture • Confined Animal Feeding Operations
Municipal Discharges/Sewage • Domestic Wastewater Treatment Plant
3. Results
3.1.0 Contaminants of Concern in Water Bodies
The Federal Clean Water Act (CWA) requires states and territories of the United States to
conduct a water quality assessment of water bodies every two years to ensure water quality standards
for primary contact recreation, secondary contact recreation, aquatic life, and raw source of drinking
water designated uses. This assessment determines whether water resources comply with water
quality standards for their designated use established by every state and territories of the United States.
For water bodies that do not meet water quality standards for the designated use, the law requires to
develop an indicator parameter (see Table 4, WQS Parameter Limits) for each contaminant of concern.
This requirement is known as the "303(d) list". According to the Puerto Rico Water Quality Standards
Regulation (2019), contaminants of concern are chemical, biological, or radioactive materials found in
effluents, sediments, or other substances generated by natural phenomena or human activities.
Indicator parameters are focal contaminants of concern that are characteristic of water quality
deterioration. Each indicator parameter reflected in the 303(d) list requires a Total Maximum Daily Load
(TMDL) permit according to the water body designated use. TMDL is the total maximum amount of
effluent allocated to a specific industry of potential pollutant sources without violating the water quality
standards established for its designated use (Puerto Rico Water Quality, 2019).
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Table 4 – Water Quality Standards (WQS) Parameter Limits. The information portrayed in table 4 was gathered from the “Puerto Rico Water
Quality Standards Regulations” (2019). Pollutants Estuary Rivers, Streams, and Lakes
Bulk of Water Quality
Color Note 1 15-Pt-Co
Dissolved Exigen Not less than 5 mg/l Not less than 5 mg/l
Enteroccoci Note 9 Note 9
Fecal Coliform Note 10 Note 10
Other Pathogens - Free of Pathogens
pH 7.3-8.5 6.0-9.0
Taste and Odor Producing Substances Shall not be Present Shall not be Present
Temperature 32.2 °C 32.2 °C
Total Dissolved Solids - 500 mg/l
Turbidity 10 nephelometric turbidity units 50 nephelometric turbidity units
Inorganic Constituents
Chlorides - 250 mg/l
Chlorine 7.5 ug/l 11.0 ug/l
Cyanide (Free) 1.0 ug/l 5.2 ug/l
Fluroride - 4,000 ug/l
Selenium 71.14 ug/l 5.0 ug/l
Sulfates 2,800 mg/l 250 mg/l
Sulfide 2.0 ug/l 2.0 ug/l
Total Ammonia Nitrogen - Note 13
Total Nitrogen 5,000 ug/l Note 11
Total Phosphorus 1,000 ug/l Note 12
Organic Constituents
Surfactants (Methyle Chloride) 500 ug/l 100 ug/l
Metals Constituents
Aluminum - 87.0 ug/l
Antimony 640.0 ug/l 5.06 ug/l
Arsenic 36.0 ug/l 10.0 ug/l
Cadmium 8.85 ug/l Note 1
Chromium III - Note 2
Chromium VI 50.0 ug/l 11.0 ug/l
Copper 3.73 ug/l Note 3
Lead 8.52 ug/l Note 6
Mercury 0.051 ug/l 0.050 ug/l
Nickel 8.28 ug/l Note 4
Silver 2.24 ug/l Note 5
Thallium 0.47 ug/l 0.24 ug/l
Zinc 85.62 ug/l Note 7
9
Water Quality Standards Parameter Limits’ notes were gathered from the “Puerto Rico Water Quality
Standards Regulations” (2019).
Note 1 - Concentration in ug/l must not exceed the numerical value given by e(0.7409 [Ln Hardness] –4.719 )
Note 2 - Concentration in ug/l must not exceed the numerical value given by e(0.8190 [Ln Hardness] +0.6848)
Note 3 - Concentration in ug/l must not exceed the numerical value given by e(0.8545 [Ln Hardness] -1.702 )
Note 4 - Concentration in ug/l must not exceed the numerical value given by e(0.8460 [Ln Hardness]+ 0.0584 )
Note 5 - Concentration in ug/l must not exceed the numerical value given by e(1.72 [Ln Hardness] – 6.59 )
Note 6 - Concentration in ug/l must not exceed the numerical value given by e(1.273 [Ln Hardness] – 4.705 )
Note 7 - Concentration in ug/l must not exceed the numerical value given by e(0.8473 [Ln Hardness] + 0.884)
Note 8 – Shall not be altered, except by natural phenomena as defined under this regulation.
Note 9- The Enterococci density, in terms of geometric mean shall not exceed 35 colonies/100mL in any 90-day interval:
neither the 90th Percentile of the samples taken shall exceed 130 colonies/100mL in the same 90-day interval.
Note 10- In shellfish growing area or harvesting areas, designated by the pertinent agency and adopted by the Board,
through Resolution: the median fecal coliform concentration of a series representative samples of the water taken
sequentially, shall not exceed 14 Most Probable Number (MPN)/100mL, and not more than 10 percent of the samples shall
exceed 43 MPN/100mL.
Note 11- Shall not exceed 1,700 ug/L in any stream nor exceed 400 ug/L in any reservoir or lake.
Note 12 – Total Phosphorus shall not exceed 160 ug/L in any river and stream nor exceed 26 ug/L in any reservoir or lake.
Note 13 - Shall not exceed the concentration in mg/L calculated using the following equation:
𝑇𝐴𝑁=0.8876 × (0.02781+ 107.688−𝑝𝐻+ 1.19941+ 10𝑝𝐻−7.688) × (2.126 ×100.028 × (20−𝑇) Where: T = temperature in °C.
10
3.1.1 River and Streams
According to the Puerto Rico Impaired Waters List (2018), 5,036.6 miles of rivers and streams
were assessed for primary and secondary contact recreation and 5,052.8 miles for the raw source of
drinking water designated uses. For primary and secondary contact recreation, the data indicates that
75.9 miles (1%) of the water bodies assessed did not have enough information to determine if water
quality standards were impaired, 2,509.4 miles (50%) were impaired with a Total Maximum Daily Load
(TMDL) permit approved, and 2,451.3 miles (49%) were impaired without a TMDL completed. For raw
source of drinking water, the water quality evaluation suggests that 263.7 miles (5%) of rivers and
streams meet all the water quality standards, 2,182.5 miles (43%) did not have enough information to
determine if water quality standards were impaired, and 2,606.6 miles (52%) were impaired without a
TMDL completed. (Table 5). The data obtained from the assessment reveals that the leading water
quality impairments were due to enterococci, turbidity, total phosphorus, and total nitrogen (Table 6).
Table 5 – Water Quality Standards Assessment for Rivers and Streams. The information portrayed in table 5 was gathered from the
“Puerto Rico Impaired Waters List” (2018), which is found at the Environment Protection Agency website.
The water attainment categories are found at the Environmental Protection Agency website under “The Integrated Reporting Guidance CWA Sections 303(d), 305(b)” (2019). Category 1: Unimpaired or Restored Waters. Waters meets all designated uses. Category 2: Waters meets some designated uses. Category 3: Waters for which not enough data or information available to determine if water quality standards are impaired. Category 4:
4a – Water is impaired with an approved TMDL. 4b – Water is impaired without TMDL, and with appropriate 4b plan. 4c – Water is impaired due to pollution not caused by a pollutant (e.g., aquatic life use is not supported due to hydrologic alteration or habitat alteration).
Category 5: Water is impaired (or threatened) without a TMDL completed.
Primary and Secondary Contact Recreation Designated Use
Water Body Type Attained Category Total
Assessed 1 2 3 4a 4b 4c 5
River and Streams 0 0
75.9 miles
2,509.4 miles
0 0 2,451.3 miles
5,036.6 miles
Raw Source of Drinking Water Designated Use
Water Body Type Attained Category Total
Assessed 1 2 3 4a 4b 4c 5
River and Streams 263.7 miles
0 2,182.5 miles
0 0 0 2,606.6 miles
5,052.8 miles
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Table 6 – River and Streams Contaminants of concern. The information portrayed in table 6 was gathered from the “Puerto Rico Impaired
Waters List” (2018), and “Puerto Rico Water Quality Standards Regulations” (2019), which are found at the Environment Protection Agency website.
Cause of Impairments Primary and Secondary
Contact Recreation Designated Use
Raw Source of Drinking Water Designated Use
Size of Water Impaired
(miles)
Bulk of Water Quality X- indicator Parameter*
pH X 208.4
Enterococci X X 2,451.3
Low Dissolved Oxygen X 1,064.9
Thermal Modifications X 33.8
Total Fecal Coliforms X 9.9
Turbidity X X 2,123.1
Inorganic Constituents
Ammonia X X 128.6
Free Cyanide 578.4
Total Nitrogen X X 1,269.3
Total Phosphorus X X 1,937.3
Organic Constituents
Pesticides X X 495.5
Surfactants (Methylene Chloride) X X 212.6
Metals Constituents
Arsenic X X 3.5
Cadmium X 54.7
Copper X 1,013.2
Lead X 434.6
Mercury X X 55.8
Silver 14.6 * See Table 4, WQS Parameter Limits
3.1.2 Lakes (reservoirs)
According to the Puerto Rico Impaired Waters List (2018), 136.1 miles of Lakes were assessed
for primary and secondary contact recreation, and raw source of drinking water designated uses. For
primary and secondary contact recreation, the data indicates that 136.1 miles (100%) of the water
bodies assessed were impaired with a Total Maximum Daily Load (TMDL) permit approved. For the
raw source of drinking water, the water quality evaluation suggests that 136.1 miles (100%) of the water
bodies assessed were impaired without a TMDL completed (Table 7). The data obtained from the
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assessment reveals that the leading water quality impairments were due to low dissolved oxygen, total
phosphorus, pH, and pesticides. (Table 8).
Table 7 – Water Quality Standards Assessment for Lakes (reservoirs). The information portrayed in table 7 was gathered from the “Puerto
Rico Impaired Waters List” (2018), which is found at the Environment Protection Agency website.
The water attainment categories are found at the Environmental Protection Agency website under “The Integrated Reporting Guidance CWA Sections 303(d), 305(b)” (2019). Category 1: Unimpaired or Restored Waters. Waters meets all designated uses. Category 2: Waters meets some designated uses. Category 3: Waters for which not enough data or information available to determine if water quality standards are impaired. Category 4:
4a – Water is impaired with an approved TMDL. 4b – Water is impaired without TMDL, and with appropriate 4b plan. 4c – Water is impaired due to pollution not caused by a pollutant (e.g., aquatic life use is not supported due to hydrologic alteration or habitat alteration).
Category 5: Water is impaired (or threatened) without a TMDL completed.
Table 8 – Lakes (Reservoirs) Contaminants of concern. The information portrayed in table 8 was gathered from the “Puerto Rico Impaired
Waters List” (2018), and “Puerto Rico Water Quality Standards Regulations” (2019), which are found at the Environment Protection Agency website.
Cause of Impairments
Primary and Secondary Contact
Recreation Designated Use
Raw Source of Drinking Water Designated Use
Size of Water Impaired (miles)
Bulk of Water Quality X- indicator Parameter*
pH X 88.4
Low Dissolved Oxygen X 136.1
Turbidity X X 34.0
Inorganic Constituents
Total Nitrogen X X 26.8
Total Phosphorus X X 134.4
Organic Constituents
Pesticides X X 48.8
Surfactants (Methylene Chloride) X X 6.9
Metals Constituents
Arsenic X X 21.9
Copper X 25.9
Lead X 7.2 * See Table 4, WQS Parameter Limits
Primary and Secondary Contact Recreation Designated Use
Water Body Type Attained Category Total
Assessed 1 2 3 4a 4b 4c 5
Lakes (reservoirs) 0 0 0
136.1 miles
0 0
136.1 miles
Raw Source of Drinking Water Designated Use
Water Body Type Attained Category Total
Assessed 1 2 3 4a 4b 4c 5
Lakes (reservoirs) 0 0 0 0 0 0
136.1 miles
136.1 miles
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3.1.3 San Juan Bay Estuary
According to the Puerto Rico Impaired Waters List (2018), 122.6 miles of the San Juan Bay
Estuary were assessed for primary and secondary contact recreation, and 55.9 miles for raw source of
drinking water designated use. For primary and secondary contact recreation, the data indicates that
122.6 miles (100%) of the water assessed were impaired without a Total Maximum Daily Load (TMDL)
completed. For the raw source of drinking water designated use, the water quality evaluation suggests
that 55.9 miles (100%) of the water assessed was impaired without a TMDL completed (Table 9). The
data obtained from the assessment reveals that the leading water quality impairments were due to pH,
enterococci, low dissolved oxygen, thermal modifications, turbidity, total phosphorus, total nitrogen,
ammonia, and oil and grease (Table 10).
Table 9 – Water Quality Standards Assessment for San Juan Bay Estuary. The information portrayed in table 9 was gathered from the
“Puerto Rico Impaired Waters List” (2018), which is found at the Environment Protection Agency website.
Primary and Secondary Contact Recreation Designated Use
Water Body Type Attained Category Total
Assessed 1 2 3 4a 4b 4c 5
San Juan Bay Estuary
0 0 0 0 0 0 122.6 miles
122.6 miles
Raw Source of Drinking Water Designated Use
Water Body Type Attained Category Total
Assessed 1 2 3 4a 4b 4c 5
San Juan Bay Estuary
0 0 0 0 0 0 55.9 miles
55.9 miles
The water attainment categories are found at the Environmental Protection Agency website under “The Integrated Reporting Guidance CWA Sections 303(d), 305(b)” (2019). Category 1: Unimpaired or Restored Waters. Waters meets all designated uses. Category 2: Waters meets some designated uses. Category 3: Waters for which not enough data or information available to determine if water quality standards are impaired. Category 4:
4a – Water is impaired with an approved TMDL. 4b – Water is impaired without TMDL, and with appropriate 4b plan. 4c – Water is impaired due to pollution not caused by a pollutant (e.g., aquatic life use is not supported due to hydrologic alteration or habitat alteration).
Category 5: Water is impaired (or threatened) without a TMDL completed.
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Table 10 – San Juan Bay Estuary Contaminants of concern. The information portrayed in table 10 was gathered from the “Puerto Rico Impaired
Waters List” (2018), and “Puerto Rico Water Quality Standards Regulations” (2019), which are found at the Environment Protection Agency website.
Cause of Impairments Primary and Secondary
Contact Recreation Designated Use
Raw Source of Drinking Water Designated Use
Size of Water Impaired (miles)
Bulk of Water Quality X- indicator Parameter*
pH X 122.6
Enterococci X 122.6
Fecal Coliforms X 47.9
Low Dissolved Oxygen X 122.6
Thermal Modifications X 122.6
Turbidity X X 122.6
Inorganic Constituents
Ammonia X X 103.8
Selenium X 18.8
Total Nitrogen X X 103.8
Total Phosphorus X X 122.6
Organic Constituents
Oil and Grease X 122.6
Surfactants (Methylene Chloride) X X 66.7
Metals Constituents
Arsenic X X 18.8
Copper X 66.7
Lead X 66.7
Mercury X X 66.7 * See Table 4, WQS Parameter Limits
4. Discussion
Water quality deterioration is a direct consequence of physical, geochemical, and biological
forces that regulate the release, transport, and fate of a range of chemical substances. These
processes may be influenced by natural phenomena or human activities (Groundwater, 1990). After
evaluating the data obtained from the Puerto Rico Impaired Waters List (2018), the foremost common
causes of water quality deterioration in rivers, streams, lakes (reservoirs), and the San Juan Bay
Estuary are turbidity, total nitrogen, and total phosphorus. The excess of nutrients and turbidity that
affected the water quality standards in these water bodies can be attributed in part to the natural
phenomena Hurricane Maria. Heavy rains on the night of September 20, 2017, caused more than
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40,000 landslides in the interior mountainous region of the island. One of the significant adverse
impacts of landslides is the transport of vast quantities of sediments to water bodies (Landslides, 2018).
According to the Puerto Rico Impaired Waters List (2018), another prime source of pollution was
domestic wastewater (onsite wastewater systems), impairing 5214.5 miles (20%) of rivers, streams,
lakes, and the San Juan Bay Estuary. The second leading source of pollution was confined animal
feeding operations (CAFO) impacting water quality standards in 3798.8 a mile (15%) of rivers, streams,
lakes, and the San Juan Bay Estuary (Table 11).
Table 11 – Potential Sources of Pollution. The information portrayed in table 11 was gathered from the “Puerto Rico Impaired Waters List”
(2018), which is found at the Environment Protection Agency website.
Potential Sources of Pollution
Rivers and
Streams Lakes
San Juan Bay Estuary
Total Miles
Size of Water Impaired (miles)
Agriculture 2613.5 90.2 - 2703.7
Collection System Failure 3029.6 36.4 122.6 3188.6
Confined Animal Feeding Operations 3609.2 67.0 122.6 3798.8
Industrial Discharges (Minor/Major) 2809.3 33.8 37.6 2880.7
Landfill 2037.7 15.0 55.9 2108.6
Marinas and Recreational Boating - - 18.8 18.8
Municipal Discharges (Minor/Major) 1752.0 12.7 18.8 1783.5
Onsite Wastewater Systems (Septic Tanks) 5011.7 136.1 66.7 5214.5
Package Plants 344.0 2.6 - 346.6
Surface Mining 615.8 - - 615.8
Unknown Source 4.8 - - 4.8
Urban Runoff/ Storm Sewers 3034.7 7.2 122.6 3164.5
4.1.0 Sources of Pollution
As defined in the Puerto Rico Water Quality Standards Regulations (2019), a source of pollution
is any activity, building, structure, facility, or vessel that generates, emits, unloads, stores, or transports
pollution. Pollution sources are classified as a point or non-point sources. A point source refers to any
visible, confined, and discrete transport from which pollutants are discharged. Effluents from point
sources include domestic wastewater treatment plants, industrial processes, and concentrated animal
feed operations and are regulated by a permit program called National Pollutant Discharge Elimination
16
System (NPDES Permit, 2016). Non-point sources of pollution are wastewater discharges from
stormwater runoff, cultivated crops, pastures, and forest lands. Most pollution problems are considered
non-point sources because they are difficult to identify, measure, manage, and control (NPDES Permit,
2016).
4.1.1 Domestic Wastewater Treatment Plants
The main objective of wastewater treatment plants is to accelerate the natural processes of
water purification by eliminating contaminants, pathogens, and chemicals (Table 12). Wastewater
treatment plants collect effluents from homes, businesses, and industries for treatment. Following
treatment, the water could be reintroduced to natural water systems, applied to the land, or reused
beneficially. As mentioned, domestic wastewater treatment includes a combination of physical,
chemical, and biological processes to remove solids, organic matter, bacteria, and nutrients dissolved
or suspended in its effluents (Inventario de Recursos, 2005).
After treatment, these effluents are discharged mainly to the ocean (primary treatment), as well
as streams, rivers, lakes (reservoirs), and estuaries. This volume of water constitutes a significant
resource with the potential reuse for diverse activities, including agricultural irrigation, and aquifer
recharge (Inventario de Recursos, 2005).
The primary treatment is the sediment filtration process. Secondary treatment processes can
eliminate up to 90% of the organic matter in the wastewater (Primer for Municipal, 2004). First, it goes
through nitrification by injecting oxygen and allowing microbes to decompose organic matter, producing
ammonium and nitrate as a byproduct. Then, it goes through an anaerobic process known as
denitrification to convert the nitrate into nitrogen gas. In the tertiary process, water is sent to the clarifiers
where the organic matter is separated. The organic matter is taken to the sludge stabilization area
where it is stabilized and converted to bio-solids that could go to land fields, agriculture land
applications, or incinerated (Primer for Municipal, 2004).
17
Finally, the water is filtered to remove any additional organic matter particles, then is chlorinated
and transferred to a storage tank to be tested and ensure that it meets all the water quality regulation
requirements. If not, the water will go through the whole process again. A significant challenge facing
wastewater treatment plants today is that the facilities are old and in need of modernization (Primer for
Municipal, 2004). Traditional wastewater treatment plants should be modernized to manage changes
in the flow and composition of wastewater better, reduce operating costs, and comply with the newer
and stricter regulatory standards on effluent discharge limits (Gernaey, K. V. et al., 2015).
A cost-effective method that could be implemented to mitigate pollution in water systems is
constructed wetlands. Constructed wetlands help reduce the excess nutrients and other contaminants
that reach water bodies. Wetlands are large basins that provide a sink for sediments and nutrients,
reduce the energy of flowing water, allowing time for various nutrient cycles to mitigate unwanted
pollutants. Constructed wetlands induce sedimentation of particulate P, making it available for plant
uptake. Wetlands are even more efficient at removing nitrogen. When nitrogen-enriched water enters
the wetland, anaerobic microorganisms use the nitrogen excess for respiration, reducing it to gas and
releasing it to the atmosphere (A Handbook, 1995).
Another approach for reducing nutrient pollution is proper nutrient management. Nutrient
management should include the “Four R’s”: apply the right nutrient, at the right rate, at the right time,
and in the right place for the chosen crop (Liu, Guodong, et al., 2018). Controlled-release fertilizers
(CRF) and slow-release fertilizers (SFR) are methods to reduce nutrient losses. Controlled-release
fertilizers are coated with inorganic or organic material, which controls the rate and duration of nutrient
release. These fertilizers are water-soluble and manufactured to meet a specific crop’s nutrient
requirements. Slow-release fertilizers include green manures, cover crops, and animal manures (Liu,
Guodong, et al., 2018).
18
Table 12 – Wastewater Treatment Plants Contaminants of Concern. The information portrayed in table 12 was gathered from “Literature
Review of Contaminants in Livestock and Poultry Manure and Implications for Water Quality” (2013) ,“Primer for Municipal Wastewater Treatment Systems” (2004), and “Puerto Rico Water Quality Standards Regulations” (2019), which are found at the Environment Protection Agency website.
Pollutants Primary and Secondary
Contact Indicator Parameter
Raw Source of Drinking Water Indicator Parameter
Potential Impacts
Bulk of Water Quality
pH X Can lead to a decrease in aquatic life
Enterococci X Fauna, aquatic, and human health effects
Low Dissolved Oxygen X Can lead to a decrease in aquatic life
Other Pathogens X X Fauna, aquatic, and human health effects
Thermal Modifications X Can lead to a decrease in aquatic life
Turbidity X X Suspended solids and cloudiness
Inorganic Constituents
Ammonia X X Aquatic life toxicity at elevated Concentrations
Bicarbonate Increase salinity in surface and groundwater
Carbonate Increase salinity in surface and groundwater
Cyanide X X Fauna, aquatic, and human health effects
Nitrate X Link to methemoglobinemia
Chlorine X Aquatic life toxicity at elevated Concentrations
Selenium X Aquatic life toxicity at elevated Concentrations
Sodium Increase salinity in surface and groundwater
Sulfate X Can lead to a decrease in aquatic life
Total Nitrogen X X Can lead to harmful algal blooms
Total Phosphorus X X Can lead to harmful algal blooms
Organic Constituents
Antimicrobials Increases antimicrobial resistance
Hormones Endocrine disruption in aquatic life
Oil and Grease X Water quality deterioration
Pesticides X X Potential endocrine disruption in aquatic life
Surfactants (Methylene Chloride)
X X Fauna, aquatic, and human health effects
Metals Constituents
Antimony X X Human health effects
Arsenic X X Aquatic life toxicity at elevated Concentrations
Cadmium X Aquatic life toxicity at elevated Concentrations
Chromium Aquatic life toxicity at elevated Concentrations
Copper X Aquatic life toxicity at elevated Concentrations
Lead X Aquatic life toxicity at elevated Concentrations
Mercury X X Human health effects
Nickel X Aquatic life toxicity at elevated Concentrations
Silver Aquatic life toxicity at elevated Concentrations
Thallium X X Human health effects
Zinc Aquatic life toxicity at elevated Concentrations
19
4.1.2 Confined Animal Feeding Operations
Confined animal feeding operations (CAFO) are agricultural operations where animals are kept,
raised, and fed in confined conditions. CAFO gather animals, feed, manure, and urine (Animal Feeding,
NRCS). Traditionally, manure was used as fertilizer applications to provide nutrients to cropland and,
as an amendment to improve soil quality. However, manure must be managed appropriately to avoid
adverse environmental impacts. CAFO effluents contain nutrients, pathogens, heavy metals,
antimicrobials, and hormones that can enter surface and groundwater (Literature Review, 2013), (Table
13).
The implementation of Best Management practices can help CAFO owners mitigate water
pollution and reuse water beneficially. Best Management Practices (BMP) are practices adapted by
farmers or urban communities to improve water quality standards (Puerto Rico Water Quality, 2019). A
Comprehensive Nutrient Management Plan (CNMP) is an essential aspect of agriculture BMPs that
could help CAFO operators comply with water quality regulations. A nutrient management plan
enhances efficiency and profitability in farm operations while preventing adverse environmental impacts
(Animal Feeding, NRCS).
Another effective method of handling animal manure is anaerobic digesters, such as covered
lagoons or fixed-film digesters. Digesters produce renewable energy and fertilizers while reducing
greenhouse gas emissions and water pollution. Also, these anaerobic biological methods can process
ten times more manure than aerobic methods, reducing odors, flies, and pathogens by 95 percent
(Manure Matters, 2006).
20
Table 13 – Confined Animal Feeding Operations Contaminants of Concern. The information portrayed in table 13 was gathered from
“Literature Review of Contaminants in Livestock and Poultry Manure and Implications for Water Quality” (2013) and “Puerto Rico Water Quality Standards Regulations” (2019), which are found at the Environment Protection Agency website.
Pollutants
Primary and Secondary Contact
Indicator Parameter
Raw Source of Drinking Water
Indicator Parameter
Potential Impacts
Bulk of Water Quality
Low Dissolved Oxygen X Can lead to a decrease in aquatic life
Pathogens X X Fauna, aquatic, and human health effects
Turbidity X X Suspended solids and cloudiness
Inorganic Constituents
Ammonia X X Aquatic life toxicity at elevated Concentrations
Bicarbonate Increase salinity in surface and groundwater
Carbonate Increase salinity in surface and groundwater
Chloride X Increase salinity in surface and groundwater
Nitrate X Link to methemoglobinemia
Selenium X Aquatic life toxicity at elevated Concentrations
Sodium Increase salinity in surface and groundwater
Sulfate X Can lead to a decrease in aquatic life
Total Nitrogen X X Can lead to harmful algal blooms
Total Phosphorus X X Can lead to harmful algal blooms
Organic Constituents
Antimicrobials Increases antimicrobial resistance
Hormones Endocrine disruption in aquatic life
Pesticides X X Potential endocrine disruption in aquatic life
Metals Constituents
Aluminum Aquatic life toxicity at elevated Concentrations
Arsenic X X Aquatic life toxicity at elevated Concentrations
Cadmium X Aquatic life toxicity at elevated Concentrations
Calcium Increase salinity in surface and groundwater
Copper X Aquatic life toxicity at elevated Concentrations
Iron Aquatic life toxicity at elevated Concentrations
Lead X Aquatic life toxicity at elevated Concentrations
Magnesium Increase salinity in surface and groundwater
Manganese Aquatic life toxicity at elevated Concentrations
Molybdenum Aquatic life toxicity at elevated Concentrations
Nickel X Aquatic life toxicity at elevated Concentrations
Potassium Increase salinity in surface and groundwater
Zinc Aquatic life toxicity at elevated Concentrations
21
5. Conclusion
In this research project, the identification of contaminants of concern and indicator parameters
for primary contact recreation, secondary contact recreation, and the raw source of drinking water
designated uses have been presented to provide an overview of impaired water bodies in Puerto Rico.
Domestic wastewater effluents contribute a substantial amount of pollution in surface and groundwater
resources in Puerto Rico. A significant challenge facing domestic wastewater treatment plants today is
that the facilities are old and need to be retrofitted. However, there are several cost-effective methods
and best management practices that could be implemented to mitigate pollution inputs in water bodies.
The information conveyed in this project could serve as an educational tool for students to learn
about different types of contaminants of concern found in wastewater effluents from the most common
point sources in Puerto Rico. Besides, this report could be considered a case study for water
conservation and planning in Puerto Rico by understanding the potential of reused water in industries
of possible sources of pollutants when treating and reusing their wastewater effluents.
There is a vast amount of data collected and analyzed on industries of potential sources of
pollution created by government agencies. Nevertheless, the general public does not benefit from this
information because the data is complicated and difficult to understand. The data compiled in this report
provides educational information to the general public in a concise and useful manner.
22
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