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Draft 2012 Pennsylvania Integrated Water Quality 

Monitoring and Assessment Report

Clean Water Act

Section 305(b) Report and 303(d) List
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Contents

Executive Summary............................................................................................................... 3

Part A: Introduction ............................................................................................................... 7

Part B: Background

Total Waters........................................................................................................................... 8

Pollution Prevention and Energy Efficiency Program........................................................... 8

NPDES................................................................................................................................... 9

Compliance and Enforcement................................................................................................10

Mining....................................................................................................................................11

Oil and Gas ............................................................................................................................11

Stormwater Discharge Permits ..............................................................................................12

Construction and Urban Runoff ............................................................................................12

Stormwater Permits Conservation Districts...........................................................................14

Combined Sewer Overflows..................................................................................................14

Nonpoint Source Control Program ........................................................................................14

Highlights of Pennsylvania’s Current NPS Program.............................................................15

Total Maximum Daily Load Development (TMDL).............................................................21

Part C: Surface Water Quality Monitoring and Assessment

Water Quality Standards Program .........................................................................................23

Plan for Achieving Comprehensive Assessments..................................................................25

Intensive Surveys...................................................................................................................26

Ambient Fixed Station Monitoring........................................................................................26

Lake Water Quality Assessments ..........................................................................................28

Citizen’s Volunteer Monitoring.............................................................................................29

Existing and Readily Available Information .........................................................................29

Assessment and Methodology ...............................................................................................31

Streams Use Support..............................................................................................................32

Record of Changes to the 2010 Integrated List 5 made in the 2012 Integrated List .............37

Lakes Use Support .................................................................................................................37

Excluding the Fishable and Swimmable Uses.......................................................................41

Lakes Trophic Status..............................................................................................................41

Lake Restoration Efforts........................................................................................................42

Lake Control Methods ...........................................................................................................43

Wetlands Protection Program ................................................................................................48

Trend Analysis for Surface Waters........................................................................................52

Part D: Groundwater

Groundwater Assessment.......................................................................................................59

USGS Releases Groundwater Quality Data for Pennsylvania...............................................60

Sources of Groundwater Contamination................................................................................61

Statewide Groundwater Protection Program .........................................................................63

Groundwater Protection Program ..........................................................................................64

Wellhead Protection and Source Water Protection Program.................................................65

Source Water Assessment and Protection Program...............................................................65
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EXECUTIVE SUMMARY

Pennsylvania has a population of 12,702,379 and area of 45,333 square miles. There are six 

major river basins - Delaware, Susquehanna, Genesee, Potomac, Ohio, and Lake Erie - with an 

estimated 86,000 stream and river miles and 161,455 lake acres. Seventeen square miles of 

Delaware Estuary and 512 acres of tidal wetlands exist in the southeast corner. In the northwest 

corner are 63 miles of Lake Erie shoreline. Scattered throughout the state are 403,924 freshwater 

wetlands. These numbers illustrate the magnitude and complexity the Pennsylvania of 

Department of Environmental Protection (DEP) faces in assessing, protecting, and managing its 

water resources. 

There are several goals of the 2012 Integrated Water Quality Monitoring and Assessment Report 

(Integrated Report). Foremost is to report on the condition of the waters in the Commonwealth. 

Other goals include describing the water pollution control and assessment/monitoring programs. 

Pollution control programs are discussed in detail in Part B, and Assessment and Monitoring in 

Part C. The report concludes with a discussion of groundwater in Part D.

Part A summarizes and discusses stream and lake assessments. The introduction describes the 

five-part list. These lists of individual waterbodies are separate from the narrative because of 

their size and are available on DEP’s website. 

In April 2007 DEP completed a ten year program to assess all wadeable streams. The census 

utilized a biological assessment of the aquatic life use. Since 2007, DEP has implemented ne 

aquatic life biological assessment methods based on the current best science. Other designated 

uses and non-wadeable waters continue to be assessed as resources and time permitted. As of 

this report 84,571 miles of streams and rivers are assessed for aquatic life use with 67,972 miles 

listed as attaining that water use. Of the impaired miles, 9,801 require development of a Total 

Maximum Daily Load (TMDL) to reduce pollutant inputs and 6,490 have an approved TMDL. 

An additional 62 miles are under compliance agreements and expected to improve within a 

reasonable amount of time. The two largest problems are agriculture and abandoned mine 

drainage. The largest stressors are siltation and metals. However, other problems should not be 

minimized because in local areas they may impact a relatively large percentage of waters. For 

example, urban runoff/stormsewers is a minor problem in rural areas but major in metropolitan 

regions. 

There are 80,525 acres of lakes assessed for aquatic life use and 43,194 acres are attaining that 

use. Of the impaired acres, 5,420 require a TMDL, 11,366 have an approved TMDL, and 20,544

acres are impaired but do not require a TMDL because they are not affected by pollutants. The 

largest problem source is agriculture and largest stressors are nutrients, suspended solids, and 

organic enrichment/low D.O. As discussed above, smaller problems should not be minimized 

because they still have regional importance. 

To protect the health of those who consume fish caught in the Commonwealth, DEP monitors 

fish flesh for possible contaminants. When concentrations of substances known to be harmful to 

humans reach action levels, fish consumption advisories are issued to inform people of the 

possible dangers and the actions they can take to protect themselves. Currently there are 

approximately 1,318 miles of fish consumption advisories in need of TMDLs and 704 with 
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approved TMDLs. Lake listings include 40,405 acres requiring TMDLs and an additional 5,664

with approved TMDLs. There is a statewide fish consumption advisory of no more than one 

meal per week for all waters to protect against the ingestion of unconfirmed contaminants. The 

fish consumption listings in this report have triggered action levels more restrictive than the one 

meal per week. It should be noted that DEP directs much of its fish tissue sampling to areas 

where there is a greater chance of problems. As a result, it is not surprising to see a higher 

number of stream miles and lake acres impaired for this use compared to the stream miles 

(3,323) and lake acres (28,765) attaining this use. 

Aquatic life use was the original focus of the statewide surveys because with a rapid and efficient 

biological assessment of aquatic macroinvertebrates (insects, snails, clams, etc.) it was possible 

to canvas the state over a ten year period. In addition, aquatic life use is a good measure because 

it is reliable as an indicator of long term pollution problems. Since completing the statewide 

census for aquatic life use, DEP is emphasizing developing assessment methodologies, 

programs, and partnerships to increase recreational and potable water supply use assessments. 

Of the 2,422 stream miles assessed for recreational use, 1,205 were attaining. There are 1,209

impaired miles requiring a TMDL and 8 with an approved TMDL. Lake recreational use was 

assessed for 81,959 acres with 76,836 attaining, and 5,123 impaired requiring a TMDL. The 

potable water supply use was assessed for 3,357 stream miles with 3,194 attaining, 151 impaired 

requiring a TMDL, and 12 with approved TMDLs. Lake potable water supply use was assessed 

for 57,953 acres with 57,941 attaining, and 12 impaired requiring a TMDL.

Part B is the narrative describing the Commonwealth’s water pollution control programs. The 

section begins with a description of efforts to prevent pollution before it becomes a problem. On 

other fronts, DEP has programs to encourage reduction in pollution that also provide cost savings 

to the treatment facilities. Examples of these successes are provided. 

As evident in the Part B narrative, the Commonwealth’s permitting and NPDES program is 

complex and deals with a large number of inspections and permits including regulating and 

permitting treatment facilities for 9,168 industrial and sewage dischargers. Pennsylvania is a 

large producer of coal and natural gas and all mining and extraction activities require permits and 

inspection. It is DEP ’s responsibility to issue permits that assure stormwater from earthmoving 

and construction activities is managed properly so as not to cause damage to streams or 

adversely affect their hydrology. County conservation districts work with DEP on stormwater 

protection. DEP also regulates combined sewer overflows (CSO) and manages and protects 

wetlands. 

Part B also includes a discussion of non-point source programs. Pennsylvania’s Non-point 

Source (NPS) Program was developed in response to Section 319 of the federal Clean Water Act 

to address problems caused by pollution from non-point sources. Unlike point source pollution, 

which comes from pipes, the causes of non-point source pollution can be difficult to define or 

quantify. Sometimes referred to as “polluted runoff,” non-point source pollution is generally 

caused by stormwater runoff across the land or infiltration of pollutants into the groundwater. 

Non-point source problems require treating and controlling runoff from large areas. Treatment 

and control is accomplished through what are known as best management practices (BMP). 

BMPs are often specifically adapted to a particular location and problem. Examples include 

improving farming practices, reclamation of abandoned mines, installation of sediment ponds, 
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and planting riparian buffers. A major function of the non-point source program is to identify 

the need for and initiate funding of BMP projects. In addition, the non-point source program

since 2007 has been identifying improving waters to potentially delist from Category 5 to 

Category 2, and as a result 89 stream miles were identified as being restored and moved from 

Category 5 to Category 2.

The non-point program works with the TMDL program. A TMDL model outputs a load 

reduction of, for example, sediment. That sediment load reduction must be achieved to meet 

water quality goals and the reductions are achieved through the use of non-point BMPs. The nonpoint program provides technical assistance, education, and funding necessary to put the BMPs 

in place. Education is an important facet of the non-point program. It often takes a consortium of 

interested and active people concerned about their watershed to achieve non-point source 

controls. The purpose and goals of the TMDL program are outlined following the section on the 

non-point program.

Growing Greener II funds were exhausted in 2009, however multiple funding sources that 

include Section 319, Growing Greener I, USDA Farm Bill funds and Conservation Reserve 

Enhancement Program (CREP) fund are important to the success of non-point source controls 

and programs as illustrated in the Part B narrative. In 2010 and 2011 these programs funded 

numerous BMP and restoration projects. 

The combined efforts of the NPDES and non-point programs to identify and correct problems 

have resulted in many water quality improvements. In 2007, DEP began an ongoing process of 

identifying areas where restoration efforts were underway and targeting them for monitoring. 

When monitoring indicates the waters are restored, Department biologists document the 

improvements and remove the problem from Category 5 of the List (impaired waters requiring a 

TMDL) and place it in Category 2 (waters attaining at least one use). Twenty-four such sites 

were identified and sampled in 2010/2011. 

Part C is the Surface Water Quality Monitoring and Assessment discussion. It begins with a 

discussion of the Water Quality Standards Program which includes water uses, water quality 

criteria, and Pennsylvania’s Antidegradation Program. 

The next three sections discuss monitoring programs including intensive surveys, ambient fixed 

station monitoring at Water Quality Network (WQN) sites, and lake monitoring.

Citizen Volunteer Monitoring Program (CVMP) is an important program with the goal of 

working with interested groups in projects that generate quality assured data related to DEP’s 

highest priorities. Ongoing projects include: bacteria sampling with the intent of assessing 

streams for recreational use and monitoring the effects of restoration efforts with the intent of 

tracking the improving water quality of streams and lakes.

EPA’s Integrated Listing guidance requires states to gather and use all existing and readily 

available data generated by sources outside DEP. This data must meet quality assurance and 

procedural guidelines outlined by DEP. Data solicitations were sent to over 500 outside sources 

in an effort to satisfy this requirement. 

The Assessment and Listing Methodology is a collection of protocols used to conduct field 

surveys and evaluate information for assessments. These protocols are the basis for the streams 
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and lakes information contained in the Integrated Report narrative and the five part list. These 

protocols were subjected to peer review. Before being adopted, the entire methodology was 

made available for public review during the summer of 2007 and spring 2009. The methodology 

is lengthy and as a result is reported separately from this narrative and is available on DEP’s 

website along with the responses to public comment.

The next several sections present detailed tables summarizing stream and lake use support. These 

tables formed the basis for the discussions presented at the beginning of the Executive Summary. 

The lakes section also contains discussions on restoration and control efforts. Some funding is 

available from DEP to restore and/or protect lakes. Control measures are codified in DEP's Rules 

and Regulations at Section 96.5 - Discharges to Lakes, Ponds, and Impoundments, which sets 

forth treatment requirements for point source discharges necessary to control eutrophication. 

Both efforts are important in protecting and restoring the Commonwealth’s lakes. Section C 

ends with an overview of wetlands that describes the types of wetlands found, DEP’s jurisdiction 

and responsibility to protect wetlands, and other wetland related activities.

Finally, Part D provides an overview of the groundwater program including assessment activities 

and wellhead and source water protection.
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PART A: INTRODUCTION

This report is the twenty-first in a series of reports prepared in response to Section 305(b) of the federal 

Clean Water Act that requires states to provide an assessment of water quality. These reports are 

prepared on a biennial basis.

DEP uses an integrated format for Clean Water Act Section 305(b) reporting and Section 303(d) listing. 

The “2012 Pennsylvania Integrated Water Quality Monitoring and Assessment Report” satisfies the 

requirements of both Sections 305(b) and 303(d). The narrative that follows contains summaries of 

various water quality management programs including water quality standards, point source control, and 

nonpoint source control. It also includes descriptions of programs to protect lakes, wetlands, and 

groundwater quality. A summary of the use support status of streams and lakes is also presented in the 

narrative report.

In addition to this 305(b) narrative, the water quality status of Pennsylvania’s waters is presented using a 

five-part characterization of use attainment status. The listing categories are:

Category 1: Waters attaining all designated uses.

Category 2: Waters where some, but not all, designated uses are met. Attainment status of the 

remaining designated uses is unknown because data are insufficient to categorize the water.

Category 3: Waters for which there are insufficient or no data and information to determine if 

designated uses are met.

Category 4: Waters impaired for one or more designated uses but not needing a total maximum daily 

load (TMDL). These waters are placed in one of the following three subcategories:

Category 4A: TMDL has been completed.

Category 4B: Expected to meet all designated uses within a reasonable timeframe.

Category 4C: Not impaired by a pollutant and not requiring a TMDL.

Category 5: Waters impaired for one or more designated uses by any pollutant. Category 5 includes 

waters shown to be impaired as the result of biological assessments used to evaluate aquatic life use. 

Category 5 constitutes the Section 303(d) list EPA will approve or disapprove under the Clean Water 

Act. 

Each waterbody must be assessed for four different uses as defined in DEP 's rules and regulations at 25 

Pennsylvania Code Chapter 93 (Water Quality Standards) in Section 93.3 Protected Water Uses. The 

four include: Aquatic Life, Water Supply, Fish Consumption, and Recreation. Generally, Aquatic Life 

pertains to maintaining flora and fauna indigenous to aquatic habitats; Water Supply relates to the 

protection of ambient water quality for possible use as a potable water supply; Fish Consumption 

protects the public from consuming tainted fish; and Recreation relates to water contact and boating. 

Each use may have different water quality criteria for individual chemical constituents and each use 

requires a different type of stream or lake assessment.

DEP encourages use of the Internet to view the Integrated Report documents electronically on its 

website at http://www.portal.state.pa.us/portal/server.pt/community/dep_home/5968, search keyword 

“Water Quality List”. Full address is:

http://www.portal.state.pa.us/portal/server.pt/community/water_quality_standards/10556/integrated_wat

er_quality_report_-_2010/682562

Because of the size of the five-part list, it will only be available electronically. 
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PART B: BACKGROUND

Part B1. Total Waters 

Table 1

Atlas of Surface Waters in Pennsylvania

The following information is presented to provide a perspective on Pennsylvania’s water 

resources:

State Population 12,702,379†

State Surface Area (square miles) 45,333

Number of Water Basins (major basins) 6

Total Miles of Rivers and Streams 86,000*

Number of Lakes/Reservoirs/Ponds**

-Number of Significant, Publicly Owned Lakes (subset)

3,956

219

Acres of Lakes/Reservoirs/Ponds**

-Acres of Significant, Publicly Owned Lakes (subset)

161,445††

98,942

Square Miles of Estuaries/Harbors/Bays

-Delaware Estuary

-Presque Isle Bay

17

6

Miles of Great Lakes Shore 63†††

Acres of Freshwater Wetlands 403,924

Acres of Tidal Wetlands 512

†

2010 US Census

†† Lakes and ponds greater than two acres

††† Lake Erie - Fourteen miles comprise the Presque Isle Peninsula. 

* DEP estimate based on 1:24,000 scale National Hydrography Data 

(NHD) GIS stream coverage. This 86,000 may change as the NHD is 

quality assured and corrected. 

** “Total Water Estimates for United States Streams and Lakes”, EPA, 

August 1993

Part B2.1. Pollution Prevention and Energy Efficiency Program

The DEP clearly recognizes the value of multi-media pollution prevention, resource conservation 

and efficiency in providing environmental protection. Not only does preventing pollution create 

a healthier, more sustainable environment, it also saves money, contributing to a stronger 

economy. Programs throughout the DEP are built upon the premise that not generating waste is 

preferable to dealing with waste after it is generated. 
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DEP’s pollution prevention programs help government and businesses move beyond 

compliance-based, end-of-pipe thinking to preventing pollution before it is created - effectively 

reducing adverse environmental impacts. The Office of Pollution Prevention and Energy 

Assistance (OPPEA) manages and administers programs for helping small businesses, industry, 

government, and schools to better manage their environmental impacts, reduce energy usage, and 

save money. Some major focus areas of OPPEA are economic development, indigenous energy, 

market barriers, distributed power, and green buildings. 

The Small Business Pollution Prevention Assistance Account (PPAA) loan program has funded a 

variety of pollution prevention/energy efficiency projects. Reported results for some of these 

projects are as follows:

Gautier Steel, Ltd. has reported saving 16,487 MWH (megawatt hours) of electricity, 67,287 

MCF (thousand cubic feet) of natural gas and 200,668 MGALS (megagallons) of water. 

Combined, these savings have given the company $2,021,762 in the five years since 

implementing their project.

The Small Business Advantage Grant Program (AGP) provides 50 percent reimbursement grants 

up to $7,500 to support eligible projects for eligible businesses. Each eligible business may only 

receive $7,500 per fiscal year (FY). The AGP provides reimbursement grant funding to promote 

the pollution prevention and energy efficiency practices of small businesses. Businesses must 

save 25 percent plus $1,000 annually as a direct result of implementing the grant supported 

project.

DEP’s contractor, The Pennsylvania Technical Assistance Program (PENNTAP) is working on 

projects through the Industrial Resource Centers, Manufacturing Extension Partnerships, DOE 

Industrial Assessment Centers, and the Ben Franklin Technology Partners utilizing DOE’s Save 

Energy Now and EPA’s Pollution Prevention Incentive for States funding. The projects are 

focused on economic development, improved energy efficiency, and waste reduction. As a 

means to encourage participation by businesses, PennTAP supported the commercialization of

emerging technologies for 10 businesses during 2010-11. Support consisted of technical 

consulting, website evaluations, and general marketing support for the products of emerging 

energy technology companies. Technical assistance was also provided for over 600 businesses 

in the form of on-site, web-based, telephone, and similar support activities - like evaluating the 

potential benefits of solar power installations. Waste and energy use-reduction assessments were 

performed at more than 76 businesses. The assessments included 45 walk-throughs, 29 multitargeted, and 2 comprehensive. Seven DOE industrial energy system workshops were conducted 

through Penn State's Continuing Education Program. Over 154 students and business 

representatives participated. The trainings addressed compressed air, pump, motor, and fan 

system best practices and were held at locations across Pennsylvania. PennTAP is also 

advancing the ISO50001 Energy Standards through 2 pilots in which 6 industrial partners will 

achieve certification under the standard – 2 by mid-2012 and 4 more by mid-2013.

Part B2.2 (a). NPDES

Pennsylvania implements the EPA delegated point source National Pollutant Discharge 

Elimination System (NPDES) permitting program through DEP’s six regional field offices and 

six district mining operations offices. While program development and evaluation occurs in 
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DEP’s central office, the field offices and district mining offices conduct site-specific permitting, 

monitoring, compliance, and enforcement activities. The central office also provides specialized 

assistance in the areas of policy, regulatory development, complex permitting, laboratory audits, 

safety training, treatment plant operations, enforcement, and data management.

The Toxics Management Strategy provides for a consistent statewide approach for addressing 

EPA priority pollutants and other toxic substances in the NPDES permit program. The strategy, 

parts of which are codified in a Statement of Policy, Chapter 16, is a support document to DEP’s 

toxic regulation, Section 93.8a of the rules and regulations.

In state fiscal years 2010 and 2011 (July 1, 2009 – June 30, 2011), field office staff issued the 

following numbers and types of NPDES permits: 369 new, 1,091 renewals, and 250 amendments 

for municipal or private sewage treatment plants, industrial discharges, and storm water 

facilities. Staff also issued 134 new, 442 renewals, and 40 amendments for coverage under 

stormwater general permits.

Water Quality Management (WQM) permits authorize construction and operation of sewage 

collection and conveyance systems and sewage and industrial wastewater treatment facilities. 

The field offices issued 991 WQM permits and permit amendments for sewage and industrial 

waste treatment plants in state fiscal years 2010 and 2011.

Permitting summaries for other programs follow later in the document.

Part B2.2 (b). Compliance and Enforcement

The DEP point source control program regulates approximately 9,168 sewage and industrial 

dischargers in Pennsylvania. Approximately 409 of these are considered major dischargers 

based on EPA criteria. DEP field offices maintain a staff of field inspectors, hydrogeologists, 

biologists, compliance specialists, supervisors, and managers to conduct activities including 

inspections of both NPDES and non-NPDES wastewater treatment facilities, emergency 

response, investigation of pollution incidents and complaints, and routine stream monitoring.

Approximately 7,585 facilities inspections were conducted during state fiscal years 2010 and 

2011. Generally, if environmental damage or willfulness is not involved in violations, an 

attempt is made to obtain voluntary compliance. In more serious situations, criminal, civil, or 

administrative actions may be used. DEP field offices completed 1,371 such actions in state 

fiscal years 2010 and 2011, resulting in approximately $6.4 million in penalties.

DEP’s Outreach Assistance Provider Program provided on-site training for wastewater treatment 

plant operators through 2009. Due to budget cuts, this program was ended in 2009. Permanent 

funding for the program was included in the fee package for the implementation of the Drinking 

Water and Wastewater Systems Operator Certification Program. As a result, this program is now 

in the process of restoring the wage payroll positions that were lost in 2009. The program should 

be able to provide this service again in the very near future. The priority for this program will be 

enhanced process control through on-site training of certified operators, resulting in improved 

compliance with permit requirements.
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Tracking of data on effluent quality for major dischargers is accomplished through EPA’s 

Integrated Compliance Information System (ICIS). There has been an ongoing effort to enhance 

the compliance monitoring program by automating the input of effluent limits data and discharge 

monitoring data to ICIS. In 2007, DEP implemented an electronic Discharge Monitoring Report 

(DMR) system to store monitoring data as well as a data system called the NPDES Management 

System to store permit information. These systems have significantly reduced the number of 

data elements that were electronically unavailable.

In 2008, with the intention of acquiring information through data transfers from the States, EPA 

released a “schema” (database requirements) for a subset of data elements. Approximately 20 

fields were associated with DMRs. Pennsylvania is now transferring DMR data electronically to 

ICIS, thus reducing the manual data entry burden for DEP staff. DEP has determined the 

available fields in the Commonwealth’s data systems and has mapped an additional 80 

permitting and facility elements and 10 inspection elements for automated uploads. During 

federal fiscal year 2011, DEP will extract data from State data systems to meet available EPA 

schema for uploads to ICIS. The data will include information on all 10,000+ facilities in 

Pennsylvania with NPDES permits and the approximately 2,000 permit actions taken by DEP 

annually. EPA plans to release additional schema in the years ahead. Until that time, DEP will 

continue manual entry for most of the remaining fields.

There are several checks and balances in place to ensure the quality of self-monitoring data. 

Since 2006, DEP’s Bureau of Labs (BOL) has been responsible for oversight of all 

environmental labs. BOL provides a year-end report to EPA with details and accreditation 

information. In addition, field inspectors review information and self-monitoring data during 

surveillance activities and follow up as appropriate.

Part B2.2 (c). Mining

District mining operations offices, under the direction of DEP's Bureau of Mining Programs 

(BMP), issue NPDES discharge permits for active mining operations. During federal FY 10 and 

FY 11, the following new permits were issued: 128 coal surface, 1 coal underground, 1 coal 

refuse reprocessing, 1 coal refuse disposal, and 64 industrial mineral surface permits.

Part B2.2 (d). Oil and Gas

During the two year period from January 1, 2010 to October 1, 2011, the Bureau of Oil and Gas 

Management (BOGM) and the Bureau of Point and Nonpoint Source Management issued six 

new NPDES discharge permits and four new NPDES permit for coalbed methane wastewater 

treatment facilities. There are a total of 16 active NPDES permits for coalbed methane treatment 

facilities and 18 active NPDES permits for brine treatment facilities in Pennsylvania. In 

addition, there are five stripper oil well discharges covered by the general permit, with two 

receiving Water Quality Management Part II permits and two pending a Water Quality 

Management Part II permit.

In response to the increasing need for treatment facilities to reduce the environmental impacts of 

the exploitation of natural gas resources associated with the Marcellus Shale formation, 

Pennsylvania Department of Environmental Protection (DEP), on March 18, 2011, under 
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Pennsylvania regulation 25 Pa Code §92a.61(g), sent letters to 25 Publicly Owned Treatment 

Works and Centralized Waste Treatment facilities that currently accept this wastewater calling 

for immediate twice monthly effluent monitoring for radionuclides and other parameters 

including TDS, pH, alkalinity, chloride, sulfate, bromide, gross alpha, radium 226 & 228, and 

uranium.

April 19, 2011, from the direction of Governor, the DEP called on all Marcellus Shale natural 

gas drilling operators to cease by May 19 delivering wastewater from shale gas extraction to 15 

facilities that then accepted it under an exemption from being covered by last year’s Total 

Dissolved Solids (TDS) regulations. Then in July 2011the DEP sent letters to approximately 88 

drilling operators seeking their certification that they are no longer using any of these 

“grandfathered” facilities for wastewater from deep gas production. 

Part B2.2 (e). Stormwater Discharge Permits

The 1990 Phase 1 federal stormwater regulations require NPDES permits for discharges of 

stormwater from certain municipalities and sites associated with certain industrial activities. 

Initially, there were four Pennsylvania cities (Philadelphia, Pittsburgh, Allentown, and Erie) on 

EPA’s list of municipalities needing permits for stormwater discharges from their municipal 

separate storm sewer systems (MS4s). Later, Pittsburgh and Erie were exempted from the 

stormwater permitting requirements because large areas of those cities were served by combined 

sewers and the discharges were covered by permits for the wastewater treatment plants. Phase 1 

MS4 permits for stormwater discharges were issued to Philadelphia and Allentown.

The Phase II federal stormwater regulations were published by EPA on December 8, 1999. 

These regulations require all construction activities involving cumulative earth disturbances 

greater than one acre to obtain permits. In addition areas within approximately 940 

municipalities (including those that were initially exempted) were identified as urbanized and 

operators of municipal separate storm sewer systems (MS4s) within those urbanized areas were 

required to apply for permits. The initial permits became effective on March 10, 2003. 

Including extensions, those initial permits will expire on March 15, 2013. Availability of 

Pennsylvania’s first MS4 permit renewal package was announced on September 17, 2011, and 

the deadline for submission of a renewal notice of intent (NOI) is September 14, 2012. 

Pennsylvania’s MS4 permitting program for municipalities consists of 138 individual permittees, 

595 general permittees, and 207 waivers from the permitting requirement. MS4 permits also 

have been issued to 37 institutional permittees. Of those, 14 are operating under individual 

permits and 23 are operating under general permits.

Final policies were published on June 3, 2006 for compliance and enforcement of the MS4 

permitting program (DEP document 363-4000-004).

Part B2.2 (f). Construction and Urban Runoff

This category includes two major subcategories: highway construction and new land 

development including residential, industrial, commercial, institutional, and recreational 

construction. Uncontrolled runoff from these sites has the potential to cause significant soil 

erosion and localized sediment pollution in streams.
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Standards and criteria for minimizing erosion and preventing sediment pollution are contained in 

Chapter 102 rules and regulations. These regulations apply to any earth disturbance activity, 

including land development and road, highway or bridge construction. Requirements for control 

measures and facilities are written to utilize best management practices, primarily by establishing 

design and performance standards.

Pennsylvania’s program is administered by DEP and county conservation districts through a 

delegation of DEP authorities to the conservation districts. Joint responsibilities for program 

implementation include the processing and issuance of permits, complaint investigations, site 

inspection, compliance, and enforcement. BMPs are reviewed for design and performance 

effectiveness through permit plan reviews and periodic monitoring at the construction site. Both 

DEP and the county conservation districts facilitate implementation of BMPs by conducting 

numerous training seminars and workshops for individuals, municipalities, and other parties 

engaged in undertaking earth disturbance activities.

DEP's comprehensive stormwater management policy uses existing authority to provide a 

framework for the integration of all Department stormwater management programs and promotes 

a comprehensive watershed approach to stormwater management in the Commonwealth. 

Fundamentally, the policy emphasizes the reduction of stormwater runoff generated by 

development and other activities by encouraging minimization of impervious cover, use of low 

impact development designs, and use of innovative stormwater BMPs that provide infiltration, 

water quality treatment, and otherwise more effectively manage the volume and rate of 

stormwater discharges. These stormwater BMPs and planning practices will be advanced 

through increased emphasis on DEP’s Act 167 stormwater management planning program and 

implementation of the NPDES Stormwater Discharge Associated with Construction Activity 

Permit programs and NPDES MS4 permits. 

Because of increased need and emphasis on improving water quality and protecting water 

resources through improved stormwater runoff management, DEP developed the Pennsylvania 

Stormwater Management Best Management Practices (BMP) Manual to support the 

implementation of stormwater management requirements and water quality antidegradation 

requirements. The BMP Manual provides the design standards and planning concepts to guide 

local authorities, planners, land developers, contractors, and others involved with planning, 

designing, reviewing, approving, and constructing land development projects. The BMP Manual 

also advances the most recent innovations in stormwater management, focusing on preserving 

on-site and off-site pre-construction hydraulic conditions. Volume and rate management through 

ground water infiltration, porous surfaces, and other onsite management are emphasized. Water 

quality components such as oil separators, passive wetland treatment, and other advanced 

technologies are also being emphasized and integrated into the BMP Manual.

Existing Erosion and Sediment Control (E&S) regulations found at Title 25, Chapter 102 

describe the requirements for controlling accelerated erosion and preventing sediment pollution 

from various earth disturbance activities. The purpose of Chapter 102 is to protect surface waters 

of the Commonwealth from sediment and stormwater pollution by requiring the use of best 

management practices (BMPs) that minimize accelerated erosion and sedimentation and manage 

post construction stormwater runoff, both during and after earth disturbance activities. Revised 

regulations were implemented on November 19, 2010.
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Since 1972, earth disturbance activities related to agricultural plowing and tilling, as well as, 

non-agricultural earth disturbance activities have been regulated under this Chapter by requiring 

persons to develop, implement, and maintain BMPs. New regulatory requirements also now 

address animal heavy use areas.

Amendments to the Chapter 102 regulations included new requirements for riparian buffers in 

special protection (HQ and EV) waters. Depending on the attainment status of the stream, a 

mandatory150-foot riparian buffer or riparian forest buffer must be established, converted or 

protected. In addition, voluntary 100-foot forested buffers can be established or converted.

Part B2.2 (g). Stormwater Permits Conservation Districts

DEP and county conservation districts jointly administer issuance of NPDES permits for 

stormwater discharges associated with construction activities. During calendar years 2009 and 

2010, conservation districts received, reviewed and acknowledged 2,871 Notices of Intent (NOI) 

for coverage under the statewide general permit. DEP issued 607 individual NPDES permits 

authorizing stormwater discharges from construction activities. In addition, conservation 

districts conducted 30,177 compliance-monitoring inspections at permitted and non-permitted 

sites. Conservation districts also conducted 5,539 complaint investigations, in addition to routine 

compliance inspections.

Part B2.2 (h). Combined Sewer Overflows

Combined sewer overflows (CSOs) to waters of the Commonwealth are considered point sources 

subject to NPDES permitting, compliance, and enforcement requirements. EPA has been 

regulating CSOs through the 1989 and 1994 national CSO policies that require each NPDES 

delegated state to develop and implement a state CSO control policy. DEP revised its CSO 

policy in February 2010. Under the revised policy, DEP conducts or provides for appropriate 

follow-up actions, including compliance monitoring, compliance actions, permit renewal, plan 

reviews, field inspections, water quality monitoring and enforcement as necessary to promote the 

development and implementation of Nine Minimum Controls (NMCs) and the Long Term 

Control Plan (LTCP) at each CSO facility. LTCP milestones are placed in NPDES permits with 

dates for completing them. DEP has continued to place a high priority on the permitting and 

inspection program to deal with requirements for implementation of NMCs and LTCP.

Part B2.3 (a). Non-point Source Control Program

Pennsylvania’s Non-point Source (NPS) Program was developed in response to Section 319 of 

the federal Clean Water Act to address problems caused by non-point sources, such as the 

overland flow of stormwater or infiltration of pollutants into the groundwater. The three main 

sources of non-point runoff resulting in degraded water quality in Pennsylvania are agriculture, 

abandoned mine drainage, and urban runoff. Other sources include abandoned oil and gas wells, 

construction activities, land disposal, habitat modification, hydromodification, and silviculture 

(logging practices).
15

The Clean Water Act requires each state to prepare a Management Plan for its non-point source 

program. This Management Plan outlines the program components to be used to address nonpoint source problems including a variety of non-regulatory, financial, and technical assistance 

programs needed to improve and maintain surface and groundwater quality. Pennsylvania last 

updated its NPS Management Plan in 2008.

Pennsylvania has received more than $93 million from the federal Section 319 Grant Program 

(FY 1990 - 2011). This money has been used to institutionalize a non-point source program, 

implement various innovative technologies to treat non-point source pollution problems, develop 

an educational program, and complete a large number of watershed initiatives. Other funding 

sources for non-point source pollution management include: Pennsylvania's Chesapeake Bay 

Program, the Nutrient Management Act, the County Conservation District Assistance Funding 

Program, the Stormwater Management Act Fund, the Coastal Zone Resources Program, USDA's 

Environmental Quality Incentives and Conservation Reserve Enhancement Programs, and the 

Environmental Stewardship and Watershed Protection Grant, also known as Growing Greener.

Growing Greener has provided $298.6 million in watershed grants since 1999. Local partners 

have added another $600 million from their own resources. The tremendous value of the 

program became clear to legislators, and Growing Greener funding was initially extended 

through 2012. This increased total funding to $547.7 million from the original $241.5 million 

allocated to DEP. The funding is being made possible through a $4.25-per ton tipping fee on 

solid waste disposed in Pennsylvania's municipal waste landfills. In July 2005, Growing Greener 

II was passed, which removed the 2012 sunset date on the tipping fee and increased funding for 

projects through 2010. 

Monitoring of both land treatment and water quality for a five- to ten-year period is the best way 

to document the effectiveness of non-point source pollution control efforts. Pennsylvania has 

hosted 4 of the 24 EPA Section 319 National Monitoring Projects (NMP) across the country. 

Pennsylvania NMPs include: the Swatara Creek NMP, monitoring the effect of passive treatment 

on abandoned mine drainage; the Stroud Water Research Center NMP, monitoring a riparian 

buffer project in an agricultural watershed; the Pequea and Mill Creek NMP, using a paired 

watershed approach to monitor the effectiveness of agricultural best management practices 

(BMPs); and the Villanova Urban Stormwater BMP demonstration site, monitoring a suite of 

innovative stormwater management practices. 

Four watersheds in Pennsylvania have been awarded EPA Targeted Watershed Grants: the 

Dunkard Creek Watershed, Christina River Basin Initiative, Upper Susquehanna River Basin 

Restoration, and Schuylkill River Watershed Initiative. The Targeted Watershed Grant is an 

EPA program designed to encourage successful community-based approaches and management 

techniques to protect and restore the nation’s waters.

Part B2.3 (b). Highlights of Pennsylvania's Current NPS Program

Education and Outreach

One element of the Section 319 Grant Program involves projects fully or partially directed 

towards NPS education and outreach. Two initiatives funded through the Section 319 Grant 
16

Program that are directed entirely at education and outreach at the grassroots level include the 

Pennsylvania League of Women Voters (LWV) and the Pennsylvania Association of 

Conservation Districts (PACD). Using funds from the Section 319 Grant Program, the LWV 

Water Resources Education Network (WREN) supported 11 grants of up to $5,000 each in 2011 

to enable groups of local citizens and officials to build community support for water resource 

protection. PACD’s NPS Pollution Prevention Educational Mini-Grant program provided 

funding of up to $2,500 each for 32 projects. These projects included the development of audiovisual products, exhibits or models, production of special events, marketing tools, publications, 

actual stream reclamation projects, hands-on water studies, and educational workshops.

Since 1999, the Growing Greener Program has funded nearly 200 education/outreach projects for 

a total of $12 million.

Building Capacity

DEP is working to establish a network of technical assistance providers to help watershed 

organizations effectively and efficiently achieve their watershed protection goals. These 

providers offer technical services to groups embarking on projects aimed at protecting and 

enhancing their local watersheds. Growing Greener currently supports seven technical providers.

Conservation district watershed specialists help local groups protect and improve their 

watersheds, provide expert advice to farmers and landowners for conservation practices, work 

with DEP regional staff, and help support local grant-funded restoration projects. There are now 

67 Growing Greener-funded watershed specialists working in 66 of the state’s 67 counties.

Pennsylvania’s Watershed Approach

Pennsylvania is committed to a watershed approach for water resource management. Locally 

managed and monitored watershed improvement projects are essential to enhancing, 

maintaining, and reclaiming the Commonwealth’s water resources.

More and more people are working to improve and protect Pennsylvania’s watersheds by 

learning about their watersheds and sharing that information with their neighbors, restoring water 

quality through hands-on projects, and planning for the future through water resources 

management.

DEP provides assistance to local groups planning to implement restoration measures in 

watersheds where one or more TMDLs have been identified. The goal is to help such groups 

develop implementation plans more expeditiously and in a manner that fully complies with EPA 

requirements for additional funding under the Section 319 Grant program.

Thirty-three watersheds across the state containing water bodies with water quality impairments 

caused by non-point source pollution have been targeted to have watershed-based 

implementation plans developed with funding from the Section 319 Grant program. Three more 

plans are being prepared with other funds. The watershed-based plans identify the type, number, 

and an estimated cost of best management practices needed to eliminate water quality 

impairments. This work, in turn, qualifies local sponsors to receive Section 319 Grant program 

construction funds for restoration projects that implement the TMDLs.
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Abandoned Mine Reclamation

Eliminating drainage from abandoned mines and restoring rivers and streams to a healthy state 

represent significant challenges. The vast majority of impacts result from mines and mining 

practices of the past, predating the 1977 federal Surface Mining Control and Reclamation Act 

(SMCRA).

It's estimated that in Pennsylvania alone, the cost of addressing all of the environmental impacts 

of mining activities prior to the passage of SMCRA will exceed several billion dollars. 

Therefore, it's unlikely that public funds alone will ever be sufficient to tackle this monumental 

set of problems. Considering the scope of the challenge and the resources required to mount a 

successful clean-up program, it is widely recognized that an active, cooperative partnership 

between involved citizens, academia, industry, and public agencies is essential to properly 

address acid mine drainage or abandon mine drainage (AMD).

Growing Greener has contributed significantly toward addressing AMD issues. The projected 

accomplishments of these grants include over 5,600 acres of abandoned mine reclamation and 

over 600 miles of stream improvements. In the past two years alone, Growing Greener funds 

have been used to treat over 1.2 MGD of AMD affected water by constructing 15 treatment 

systems and reclaiming 500 feet of highwalls. Additionally, the Bureau of Abandoned Mine 

Reclamation awarded reclamation contracts using Growing Greener, State Capital Budget and 

Abandoned Mine Land (AML) Program funds aimed at reclaiming 1,298 acres of abandoned 

mine lands (572 acres in 2009 and 726 acres in 2010) and installing 3 projects to reduce or treat 

Acid Mine Drainage (AMD). Two of these projects involve the construction of large active 

treatment plants, each of which can treat up to 10 MGD and together will improve more than 60 

miles of stream. 

The Western Pennsylvania Coalition for Abandoned Mine Reclamation (WPCAMR) was formed 

in 1982 by six western Pennsylvania conservation districts. Today 24 county conservation 

districts make up WPCAMR. In 1996, the Eastern Pennsylvania Coalition for Abandoned Mine 

Reclamation (EPCAMR) was formed covering 16 counties in the anthracite coal region and the 

northern bituminous region. Today EPCAMR represents a coalition of watershed organizations, 

reclamation partners, co-generation plants, the active anthracite mining industry, and regional 

non-profit organizations.

The goal of the coalitions is to provide leadership for building local watershed-based support and 

partnerships with grassroots organizations whose primary focus is abandoned mine drainage 

abatement and abandoned mine land reclamation.

An important event in the battle to address AMD occurred in December 2006 when the 

Abandoned Mine Lands (AML) Program was reauthorized in the final hours before Congress 

adjourned. The AML Reauthorization, which amends the 1977 Surface Mining Control and 

Reclamation Act (SMCRA), extends the AML Program for at least 15 years and will triple the 

AML funding Pennsylvania receives from reclamation fees collected on every ton of coal 

produced. In the next 15 years Pennsylvania should receive at least $1.5 billion to clean up 

Priority 1 and 2 AML sites. States can also set aside up to 30% of this funding to address AMD 

problems not associated with Priority 1 and 2 sites. This extra funding will increase the number 

of AML problems that can be remediate, however, it will not be enough money to address all of 

the problems in Pennsylvania.
18

The State’s Section 319 Grant program has also made a significant contribution toward 

correcting abandoned mine drainage (AMD) problems using passive treatment systems. A total 

of 16 projects costing nearly $3.2 million to treat AMD through passive treatment were funded 

through this program in 2010 and 2011.

Organizations supported by Section 319 grants, the Eastern and Western Pennsylvania Coalitions 

for Abandoned Mine Reclamation (EPCAMR and WPCAMR) and Stream Restoration, Inc., are

cooperating in inventorying and mapping AMD and AML features across the State, including 

abandoned mine lands, deep mine pools and passive treatment systems.

Agriculture and Nutrient Management

Pennsylvania’s Section 319 Non-point Source (NPS) Management Program provides significant 

financial and technical assistance resources to help reduce agricultural sources of sediment and 

nutrients to surface waters. Section 319 grants have provided $1.7 million in funding for nine 

agricultural BMP implementation projects in 2010 and 2011.

Section 319 program agricultural projects are targeted to TMDL-approved watersheds with an 

approved Watershed Implementation Plan (WIP) or watersheds with 303(d) listed streams. 

Projects continue to be implemented in WIPs for agricultural NPS-impaired watersheds include 

Core Creek/Lake Luxembourg (Bucks County); Upper Kishacoquillas Creek (Mifflin); 

Conewago Creek (Dauphin); Mill Creek (Lancaster); Codorus Creek (York); Conowingo Creek 

(Lancaster); Mill Creek/ Stephen Foster Lake (Bradford); Hungry Run (Mifflin); and Buffalo 

Creek (Union). The figure below illustrates these agricultural WIP locations. 

The NPS Program website provides detailed information on WIPs and Pennsylvania’s NPS 

Program at http://www.portal.state.pa.us/portal/server.pt?open=514&objID=554272&mode=2. 

Projects are being implemented in these watersheds to reduce impacts from nutrients, 

sedimentation/siltation, organic enrichment/low dissolved oxygen, and other causes of 

agricultural impairment. Program funds are used to develop and implement nutrient 
19

management and farm conservation plans and best management practices (BMPs) identified in 

these plans. Partnerships with the USDA-Natural Resources Conservation Service (NRCS) and 

county conservation districts assist with both plan and BMP implementation. 

Nutrient Management Program

Pennsylvania’s Nutrient Management Program, Act 38 of 2005, was revised as part of the ACRE 

program initiative unveiled in 2004. Act 38 addresses all farms requiring development of 

nutrient management plans. The Nutrient Management and CAFO programs coordinate efforts 

to ensure all farms are covered. The success of these programs is due to the partnership between 

the State Conservation Commission (SCC), PA DEP, PA Department of Agriculture, county 

conservation districts, private sector planners, and farm operators. The SCC published major 

revisions to the NMP regulations in June 2006. These revisions became effective October 1, 

2006. Nutrient management planning revisions include the manure export requirements included 

in the CAFO program, along with additional phosphorus management, manure and soil testing, 

cover crop and residue minimums for ground cover, and riparian buffer requirements. These 

revisions were phased-in on farms with existing NMPs over a three-year period ending on 

October 1, 2009. They are being implemented immediately on new or expanding operations. A 

total of 1044 CAFOs were required to have NMPs for 2010, and an additional 1,801 voluntary 

NMPs were developed. 

 

Concentrated Animal Feeding Operation Program

In October 2005, revisions to Pennsylvania’s Concentrated Animal Feeding Operation (CAFO) 

program regulations became final. This allowed Pennsylvania’s program to be consistent with 

the federal Environmental Protection Agency’s CAFO rule. A major change under the revised 

program is the extension of CAFO permit coverage to a large portion of the state’s poultry

operations. With the new requirements including dry poultry and newly covered operations, 

total accepted applications rose from 170 CAFOs in March of 2006 to 363 as of September 30, 

2011. DEP has authority to implement the CAFO program and in 2008 completed the first 

update of its permits and forms. DEP is currently pursuing re-approval for its NPDES General 

Permit. The CAFO and nutrient management website includes a CAFO application review 

guidance document and is limited to NMP supporting materials. DEP maintains an annual 

CAFO and CAO inspection goal in coordination with county conservation districts and assures 

all covered operations are following the program requirements.

Resources Enhancement and Protection Program

The Resources Enhancement and Protection Program (REAP) was created through Act 55 of 

2007. REAP allows farmers and businesses to earn tax credits in exchange for approved BMP 

implementation on agricultural operations that will enhance farm production and protect natural 

resources. Farmers receive tax credits of up to $150,000 per agricultural operation, covering 

50% or 75% of the total cost of a BMP. Farmers also qualify for a 50% tax credit for no-till 

equipment purchase. REAP funding in 2009- 2010 provided $5 million in tax credits that helped 

fund 205 BMPs, 120 equipment purchases and the development of 37 Nutrient Management/ 

Conservation /Manure Management Plans (Plans). REAP funds for 2010-2011 provided $4.5 

million for 270 BMPs, 125 equipment purchases and the development of 39 Plans. For 2011-

1012 REAP funding is at the $10 million level. The State Conservation Commission administers 

REAP and tax credits are granted through the PA Department of Revenue. 
20

Conservation Reserve Enhancement Program

Pennsylvania’s Conservation Reserve Enhancement Program (CREP) is funded through both the 

USDA-Farm Services Agency (FSA) and the PA DEP in both the Susquehanna River and Ohio 

River basins. Total enrollment in the 43 (20 lower plus 23 upper) Susquehanna River CREP 

counties has increased to 178,000 acres as of September 30, 2011. In the Ohio River CREP (16 

counties), total enrollment increased to 28,800 acres by that date. Approximately $26 million 

was provided in 2010 for financial incentives, practice installation and rental payments. A 

potential transfer of 24,000 Ohio River CREP acres to the Susquehanna River CREP is being 

considered. A CREP expansion into counties within the Delaware River basin is also being 

evaluated.

Natural Resources Conservation Service Programs

The Pennsylvania Office of the U.S. Department of Agriculture’s Natural Resources 

Conservation Service (NRCS) receives substantial funding through the federal Farm Bill for 

implementing conservation programs statewide and through the Chesapeake Bay Watershed 

Initiative. The 2010 federal Farm Bill provided increased funding for PA NRCS agricultural 

conservation program implementation. Obligated funding for FFY2010 totaled over $38 million. 

Funding was allocated to several program areas, including the Conservation Stewardship 

Program (CSP) $3.975 million, Environmental Quality Incentive Program (EQIP) $12.866 

million, Chesapeake Bay Watershed Initiative (CBWI) $9.776 million, Agricultural Management 

Assistance $0.855 million, Wetlands Reserve Program $4.100 million and Wildlife Habitat 

Incentive Program $0.822 million. A second allocation of $6.3 million in conservation funds 

was received by the PA NRCS in July 2011 and will help landowners install conservation 

practices that improve natural resources on farms, forestland, and wetland areas throughout 

Pennsylvania. The additional funds are CBWI $2.8 million, WHIP $750,000, AMA $500,000 

and WRP $2.9 million. PA NRCS accomplishments are included on the PA NRCS website at 

www.pa.nrcs.usda.gov/programs/. CBWI priority watersheds and approved practices are 

included on the website at www.pa.nrcs.usda.gov/.

Environmental Stewardship and Watershed Protection Program

The Environmental Stewardship and Watershed Protection Act of 1999 (Growing Greener I) and 

the Watershed Stewardship Act 45 of 2005 (Growing Greener II) have funded many agricultural 

and soil and water conservation related projects. Millions of dollars have also been invested 

through statewide efforts to implement agricultural BMPs through CREP, Chesapeake Bay 

Foundation initiatives, the PA Association of Conservation District Technical Assistance grants, 

and Conservation District Watershed Specialist staff. In 2010 and 2011, agricultural projects 

were funded in many counties throughout PA. A complete summary of projects and funding 

provided is available on the DEP Grants Center website at 

http://www.depweb.state.pa.us/portal/server.pt/community/growing_greener/13958 .

Stream Corridor Protection and Restoration

Natural stream channel design addresses the entire stream system. It is based on fluvial 

geomorphology (FGM), which is the study of a stream’s interactions with the local climate, 

geology, topography, vegetation, and land use - how a river carves its channel within its 

landscape. All successful natural stream channel designs address sediment transport, habitat 

enhancement, and bank and channel stabilization. Natural stream channel design (NSCD) is 
21

relatively new to Pennsylvania. Our understanding of what works best to restore a channel’s 

natural stability is still evolving, particularly across a state as diverse in geography and land use 

as Pennsylvania. The Guidelines for Natural Stream Channel Design for Pennsylvania 

Waterways were developed with funding through a Section 319 grant by the Keystone Stream 

Team, an informal group comprised of government and environmental resource agencies, 

university researchers, sportsmen, citizen-based watershed groups, and private companies. These 

guidelines are aimed at watershed organizations and professionals involved in stream restoration 

design, construction, and permitting. The guidelines can be found at 

http://www.canaanvi.org/canaanvi_web/community.aspx. 

The Keystone Stream Team used a Section 319 grant to develop a web-based database for 

reference reach information collected on NSCD projects. A Section 319 grant also enabled the 

U.S. Geological Survey to develop Regional Curves. More information on both projects is 

available on the Keystone Stream Team’s website at: www.keystonestreamteam.org.

In addition, the 319 Grant Program has provided over $800,000 in the past two years to fund ten 

projects on selected streams using NSCD techniques. 

Since 1999 Growing Greener has funded nearly 50 FGM implementation projects for a total of 

$6.2 million.

Documenting Restored Waterbodies

Significant funding has been provided over the past several years from non-point source 

programs such as Growing Greener and Section 319 in support of stream and lake assessment, 

planning, and restoration activities. Hundreds of projects have been successfully completed. 

Those activities are beginning to show water quality improvements, but efforts to document them 

have generally been localized and inconsistent.

During 2007, DEP launched a continuing effort to identify waterbodies across the state in which 

significant improvements to water quality have been observed. Stream names and locations are 

solicited from DEP watershed managers, conservation district watershed specialists, and citizen 

volunteer monitoring groups. DEP biologists then survey these water bodies to determine the 

extent of their recovery and their potential to be removed from the State’s impaired list. Analysis 

of the survey results is on-going and changes to the Integrated Report are made as they become 

available. The Department has petitioned EPA to remove 38 stream segments from Category 5 of 

the Integrated Report, as the result of this process. These delisted stream segments add up to a 

total of 89 restored stream miles.

Many other waterbodies have shown improved water quality, but have not improved enough to 

be removed from the impaired lists. As more non-point source funding is applied in these 

watersheds, it is anticipated that water quality will continue to improve and additional stream 

segments will be removed from impaired status.

Part B2.3(c). Total Maximum Daily Load Development (TMDL)

Section 303(d) waters are those waterbodies that do not or will not meet water quality standards 

even after the application of all required technology-based treatment and other pollutant control 

requirements. DEP assesses Commonwealth waters and places those impaired waters in 
22

Category 5 of the Integrated Report. Impaired waters require the development of a TMDL. A 

TMDL is the amount of pollutant loading that a waterbody can assimilate and still meet water 

quality standards. A TMDL is the sum of individual wasteload allocations (WLAs) for point 

sources, load allocations (LAs) for nonpoint sources, and a margin of safety. DEP uses 

mathematical models to develop the TMDLs.

TMDLs are planning tools that set water quality objectives for impaired waters. Meeting the 

water quality objectives of the TMDL will result in the attainment of water quality standards. If, 

however, a waterbody is found to still be impaired after meeting the TMDL objective, the TMDL 

is reconsidered and new objectives set.

TMDLs are developed for the sources and causes of impairment that are identified in Category 5 

of the Integrated Report. In the years 2010 and 2011, DEP finalized 14 TMDLs establishing 

allocations to the appropriate sources of pollutant loading. Individual WLAs are the amounts of 

the load allocated to point sources. WLAs are the basis for setting limits in National Pollutant 

Discharge Elimination System (NPDES) permits, which are the implementation procedures used 

to correct pollution problems attributed to point source discharges. The LA portion of the 

TMDL is the amount of the load that is allocated to categories of non-point sources. The LAs 

are the basis of future watershed restoration plans, which are the first part of correcting non-point 

source pollution problems.

The development of an implementation (or restoration) plan begins with a more detailed 

assessment of a watershed. The detailed assessment includes an analysis of the known water 

quality, identification of quantities and locations of pollution sources, and selection of priorities 

for corrective action. It concludes with a description of the management measures needed to 

restore and maintain water quality, and it provides for public input concerning water quality 

problems and the restoration measures needed. The result of these activities is a management 

plan that includes the goals and objectives for improving water quality, an estimate of the 

technical and financial resources needed to implement the plan, an education program, and 

monitoring to demonstrate the success of the plan. The document also includes a budget and a 

timetable for implementation that identifies interim milestones. DEP will encourage local 

groups, watershed associations, or county conservation districts to take the lead and/or play an 

active role in completing detailed assessments and developing the implementation plan. Grant 

monies from the CWA Section 319 Non-point Source Program and the Commonwealth’s 

Growing Greener program can be used to complete these assessments. The final plan should 

meet the objective set in the TMDL.
23

Part C: Surface Water Quality Monitoring and Assessment

Part C1.1. Water Quality Standards Program

Water Quality Standards (WQS) are the combination of water uses to be protected, the criteria 

(i.e. levels of substances) that need to be maintained or attained to support the uses, and an 

antidegradation policy. WQS are important elements of Pennsylvania's water quality 

management program because they set the general and specific goals for the quality of our 

waters. WQS are instream water quality goals that are achieved by imposing specific regulatory 

standards, such as treatment requirements, effluent limitations and best management practices.

Pennsylvania's WQS are found in DEP's rules and regulations at 25 Pennsylvania Code Chapter 

93 (Water Quality Standards). General or narrative criteria applicable to all waters are designed 

to control those substances not identified by specific criteria but which may be harmful to 

protected water uses or to human, animal, plant or aquatic life if present in excessive amounts. 

Specific water quality criteria are contained in Chapter 93, including criteria for toxic substances 

identified as EPA priority pollutants, as well as other substances (available electronically at 

www.pacode.com.).

Water quality standards implement the provisions of Pennsylvania's Clean Streams Law (35 P.S. 

Section 691.1 et seq.) and Section 303 of the federal Clean Water Act (33 U.S.C.A. § 1313). 

The authority of the Environmental Quality Board to promulgate and amend water quality 

standards is found in Sections 5 and 402, of the Clean Streams Law and in Section 1920-A of the 

Administrative Code of 1929 (71 P.S. Section 510-20).

Section 303(c) of the Federal Clean Water Act requires that “... the state shall from time to time 

(but at least once every three year period) hold public hearings for the purpose of reviewing 

applicable water quality standards and, as appropriate, modifying and adopting standards...” The 

review and revisions to WQS are part of Pennsylvania's continued planning process and water 

quality management program. The development and review of WQS and the complementary 

water quality assessment program consider the fundamental policies that are set forth in state and 

federal law which includes the national goal to achieve “fishable/swimmable” waters. 

Pennsylvania’s most recent triennial review (TR08) included amendments to Chapter 93 to 

incorporate updated and revised criteria for toxic substances that were previously contained in 

Chapter 16 Water Quality Toxics Management Strategy – Statement of Policy. Other 

amendments include clarifications of terms and definitions, drainage list corrections, a review of 

waterbody segments that do not meet the fishable or swimmable uses, and other corrections of 

typographic, format, and grammatical errors. In addition, DEP adopted revisions to Chapter 16 

for updates to the human health criteria methodologies and updates or corrections to the 

approved analytical methods. This triennial review of Pennsylvania’s WQS was submitted to the 

US EPA Region 3 Administrator on July 9, 2009 for review and approval following adoption as 

final rulemaking at the January 20, 2009 Environmental Quality Board (EQB) meeting, and 

publication in the Pennsylvania Bulletin on May 16, 2009 (39 Pa.B. 2523). These amendments 

are based on proposed rulemaking, with some modification, that were approved by the EQB at 

its October 16, 2007 meeting, which were published in the Pennsylvania Bulletin on January 12, 

2008 (38 Pa.B. 236, 248) with provision for a 45-day public comment period, including public 

meetings and hearings that were held at the Department’s Southcentral Regional Office in 
24

Harrisburg, PA on February 14, 2008. A correction was published in the Pennsylvania Bulletin 

on February 2, 2008 (38 Pa.B. 612) to correct the criteria for two chemicals found in the 

proposed Table 5, § 93.8c (relating to criteria for toxic substances). Based on a request received, 

the public comment period was extended an additional 30 days and closed on March 27, 2008, as 

published in the Pennsylvania Bulletin on February 23, 2008 (38 Pa.B. 976). 

EPA approval on the TR08 triennial review was received in a letter dated April 15, 2010. The 

Department is in the preliminary stages of initiating the next triennial review of Pennsylvania’s 

WQS. The scope of the next triennial review is being developed, but at a minimum will include 

consideration of updates to aquatic life and human health criteria that have been issued by EPA, 

and that were not considered during previous triennials. Exclusion of the water contact 

(swimmable) use in a portion of the Delaware Estuary (RM 108.4 to RM 81.8), and from the 

outer Erie Harbor/Presque Isle Bay harbor basin and central shipping channel will be evaluated 

to determine whether conditions still prevail that warrant these exclusions from Pennsylvania’s 

WQS. The Department is also reevaluating the existing dissolved oxygen criteria, as well as 

considering the development of new water quality criteria for pollutants not currently regulated, 

or where water uses may not be adequately protected through existing criteria. Rulemaking 

associated with the next triennial review is expected to be initiated during winter 2012, for 

completion as final rulemaking during 2013. Development of the proposed rulemaking phase 

will be shared with other affected agencies, EPA and appropriate advisory committees. Once 

proposed, the triennial review will include provision for public participation, with a period 

(minimum of 45 days) to allow for public review and comments for consideration in the 

development of final rulemaking.

The Antidegradation Implementation Guidance, completed in 2003, is designed to apply DEP’s 

antidegradation regulation, partially approved by EPA in 2000 and finally approved in 2007. 

With the completion of the guidance, U.S. Environmental Protection Agency (EPA) moved to 

formally remove its promulgation of an antidegradation regulation for Pennsylvania. EPA has 

taken final action on a 2008 proposal to withdraw the Federal antidegradation policy for all 

waters of the United States within the Commonwealth of Pennsylvania by publishing notice in 

the Federal Register on May 28, 2010 (see 75 FR 29899). EPA has withdrawn the federal 

promulgation at 40 CFR 131.32 to allow Pennsylvania to implement its own antidegradation 

policy. EPA determined that Pennsylvania has adequately demonstrated that its antidegradation 

policy protects all waters at a level consistent with the Federal requirements under the Clean 

Water Act. Therefore, the Federal promulgation became redundant. This final rule to remove 

the Federal promulgation for Pennsylvania was effective on June 28, 2010. The antidegradation 

policy, which applies to all waters, mandates that existing uses are maintained and protected, and 

that the existing quality of High Quality and Exceptional Value waters are also maintained and 

protected.

In Pennsylvania, water uses that are protected statewide include Warm-Water Fishes; Potable, 

Industrial, Livestock, Wildlife, and Irrigation Water Supply; and Boating, Fishing, Water 

Contact Sports, and Esthetics. Other uses, such as Cold-Water Fishes, Trout Stocking, High 

Quality or Exceptional Value waters, navigation, and others, are protected as applicable on a 

waterbody by waterbody basis.

Portions of only two waterbodies in the Commonwealth have been shown to not fully support the 

federal “fishable/swimmable” goal. The water contact (swimmable) use is excluded from RM 

108.4 to RM 81.8 in the Delaware Estuary because of significant impacts from combined sewer 
25

overflows, and from the outer Erie Harbor/Presque Isle Bay harbor basin and central shipping 

channel due to the hazards to recreational users posed by commercial shipping traffic.

Part C1.2. Plan for Achieving Comprehensive Assessments

In 1996, DEP developed a strategy for the statewide assessment of wadeable free-flowing 

streams involving a basic field-level biological screening assessment. After completing the firstever statewide assessment of the state’s wadeable surface waters in April 2007, DEP replaced the 

original protocol with a new, more intensive assessment protocol for the second statewide 

assessment. DEP’s new plan for achieving comprehensive, statewide assessment of its surface 

waters is based on the implementation of the Instream Comprehensive Evaluation (ICE) 

program.

The ICE program is designed to assess the water quality of previously assessed streams with a 

more rigorous methodology. It is based on a survey design that includes both probability based 

and targeted sampling within one major sub-basin in each of six DEP regions. Initial fieldwork 

began in 2005 in the Delaware drainage and was expanded to include the first set of six regional 

sub-basins in the rest of the state in 2006. A new set of six sub-basins will be surveyed upon 

completion of the previous six basins and repeated on a rotating-basin schedule thereafter. In the 

summer of 2011, 24 of 25 sub-basins have been completed for the probability based sampling. 

This is a cooperative effort led by Office of Water Management, with assessments being 

conducted by Department field and central office staff.

The ICE program uses an intensive biological assessment protocol that is a modification of 

EPA’s Rapid Bioassessment Protocol (RBP) III method, which includes laboratory identification 

of benthic macroinvertebrates to genus level and an RBP habitat assessment. Each biological 

assessment results in an Assessment Summary for input to the 305(b) assessment database and 

GIS that identifies waters with obvious aquatic life use impairment and those with no obvious 

impairment. In addition to these stream assessment projects, a lake assessment element is also 

being implemented. Lake sampling efforts are described in the Lakes Water Quality Assessment 

section.

In 2006, DEP began a potable water supply monitoring program targeting the source waters for 

community water supplies in the Commonwealth to assess attainment of the potable water 

supply use (PWS). The monitoring protocol consists of the collection of multiple grab samples 

upstream of the point of withdrawal during a 12-13 month period. Water chemistry analysis is 

completed for 9 parameters of concern for drinking water. Analysis of the 12-13 months of 

samples results in an Assessment Summary for input to the 305(b) assessment database and GIS 

that identifies waters with obvious aquatic life use impairment and those with no obvious 

impairment. In 2011, approximately 95% of PWS surface water sources have been monitored 

and assessed.

In addition to the Aquatic Life and Potable Water Supply use assessments, DEP employs a 

Bacteriological Sampling Protocol to assess surface waters for water contact recreational use 

during the swimming season. Citizen volunteers collect at least two sets of fecal coliform 

samples from streams throughout the state from May 1st through September 30th. Each set is 

comprised of a minimum of 5 samples collected within a 30 day period. The samples are 

analyzed within 6 hours of collection by a DEP accredited laboratory for an exact count of fecal 
26

coliform units to determine compliance with standards. Each recreational assessment results in 

an Assessment Summary for input to the 305(b) assessment database and GIS that identifies 

waters with obvious recreational use impairment and those with no obvious impairment. 

Part C1.3. Intensive Surveys

Intensive surveys have been a key element of DEP’s water quality assessment program since 

their inception in 1965. These chemical and biological stream and lake investigations are 

conducted to gather background or baseline data on specific streams or lakes to determine the 

effects of point and/or non-point source discharges on receiving water quality, provide data in 

support of administrative or enforcement actions, determine the source of spills of pollution 

materials and evaluate their effect on water quality, and assess the distribution and accumulation 

of trace metals and selected organics in fish tissue or sediments. These surveys can include any 

combination of chemical sampling of water, effluent, sediment, or fish tissue; flow measurement; 

qualitative, quantitative, or semi-quantitative EPA RBP macroinvertebrate sampling; qualitative 

or quantitative (RBP) habitat assessment; or qualitative (and sometimes quantitative) fish 

sampling. While the current emphasis is on evaluation of waters previously assessed as attaining 

designated uses (discussed in the previous section), other types of intensive surveys remain 

important to the Commonwealth’s water quality management program.

An important element of DEP’s water quality assessment program is the evaluation of candidate 

waters for Special Protection designation as High Quality (HQ) or Exceptional Value (EV) 

Waters. These targeted, intensive surveys involve field studies of habitat and the aquatic 

community, observation of land use, and filed and other known information to determine if a 

basin or stream segment qualifies for Special Protection in the Antidegradation program. Streams 

receiving HQ or EV designation are protected to maintain their existing quality.

Part C1.4. Ambient Fixed Station Monitoring

The Pennsylvania Water Quality Network (WQN) is a statewide, fixed station water quality 

sampling program operated by Bureau of Point and Nonpoint Source Management. It is designed 

to assess both the quality of the Commonwealth’s surface waters and the effectiveness of the 

water quality management program by accomplishing four basic objectives:

1. Monitor current status and temporal water quality trends in major surface streams (routine 

stations)

2. Monitor current status and temporal water quality trends in selected reference waters 

(reference stations)

3. Monitor current status and temporal water quality trends in major tributaries entering the 

Chesapeake Bay

4. Monitor current status and temporal water quality trends in selected lakes

Major streams are considered to be interstate and intrastate waters with drainage areas of roughly 

200 square miles or greater. These waters receive both point and non-point source pollutants and 

are sampled at or near their mouths to measure overall quality before flows enter the next higher 

order stream. In this way, current water quality status and trends can be established and the 
27

effectiveness of water quality management programs can be assessed by watershed. In addition, 

reference stations are selected to represent: 1) “ambient” waters of natural quality minimally 

affected by human activities; and 2) “typical” waters with quality representative of that normally 

found in the region of the state being sampled.

The WQN consists of 112 routine stations of which ninety-two are sampled bi-monthly and 

twenty are sampled monthly for stream discharge measurements and physical/chemical analysis. 

All routine stations are sampled every other year for biological evaluation. Twenty-six reference 

stations are generally sampled monthly for stream discharge and physical/chemical analysis and 

annually for biological evaluation. Also, thirty Chesapeake Bay Nutrient and Sediment loading 

stations are sampled monthly for stream discharge and physical/chemical analysis and every 

other year for biological evaluation. In addition, these Chesapeake Bay loading stations are 

targeted for sampling eight times per year during storm events.

Single mid-channel or spatially composite, depth-integrated samples are collected at each site 

depending on stream size. Stream discharge (flow volume) is measured or calculated each time a 

water sample is collected. United States Geological Survey (USGS) stream gauging facilities 

and/or extrapolation equations are utilized whenever possible. Where no USGS 

facilities/equations exist, stream discharge is measured by U.S. Army Corps of Engineers and 

private facilities, or calculated according to methods outlined by USGS. At a minimum, 

macroinvertebrate samples are collected every other year at both routine and Chesapeake Bay 

load monitoring stations between August 1 and October 31 and annually at reference stations 

during fall (November 1 – December 30) or spring (March 1 – April 30) utilizing DEP benthic 

sampling methodology adapted from EPA Rapid Bioassessment Protocols.

Fish tissue is sampled periodically at the rate of about 100 WQN samples per year. Sampling 

locations are determined annually. Sampling is rotated through the network to provide periodic 

complete coverage and to maintain surveillance on problem waters. Fillets are sampled for 

appropriate pollutants in order to assess suitability for human consumption.

Lakes included in the WQN (except for Lake Erie and Presque Isle Bay that are part of the base 

network) are selected after consideration of size, public access, intensity of use, and availability 

of existing data. Large lakes with heavy public use and/or historical data are favored for 

inclusion because changing trends in the water quality of these resources have the potential for 

serious impacts on water uses.

In the past, lakes have been scheduled for annual sampling in groups of 15 to 20. Lake groups 

are sampled once a year for five consecutive years before initiating a new group. The five-year 

data blocks were then used to assess lake water quality trends. Fifteen lakes are currently being 

sampled in addition to Lake Erie and Presque Isle Bay. Lake levels for Lake Erie and Presque 

Isle Bay stations are measured at the U.S. Coast Guard station at the entrance to Erie Harbor.

Lake Erie and Presque Isle Bay samples are collected at mid-depth. The other lake WQNs have 

two samples collected per site during mid-summer stratification. These sites correspond to the 

deepest point in each lake, with one sample collected one meter below the surface and the second 

sample one meter above the lake bottom. A temperature/dissolved oxygen profile is recorded 

through the vertical water column and an aliquot from the shallow sample is filtered for 

chlorophyll-a analysis.
28

Qualitative plankton samples and chlorophyll a are collected annually from Lake Erie and 

Presque Isle Bay. Quantitative invertebrate or plankton sampling and qualitative or quantitative 

fish sampling is optional at other lakes and may be conducted at the discretion of the collector.

Part C1.5. Lake Water Quality Assessments (LWQA)

Basic water quality assessments for lakes are achieved mainly through two programs in 

Pennsylvania – the Lake Water Quality Network sampling, and the TSI or Trophic State Index 

evaluations, described below.

LWQN – a statewide set of lakes is sampled once each summer for 5 years to track 

trends. A new set of 15 lakes was selected for the 2011-2015 sampling round. LWQN 

sampling is funded mainly through the 106 grant

Lake TSI studies – all six DEP Regions incorporate TSI lake surveys to determine if 

phosphorus controls are needed for point source discharges in the watershed or to 

determine current trophic status of a lake. Samples are collected three times in one year

to cover the Spring, Summer and Fall seasonal variation; each date includes a minimum 

of two stations, sampled at surface and bottom locations. Approximately 15 to 20 lakes 

per year are normally sampled using this program. Funding for these studies is through 

the 319 Program, and the State’s Clean Water Fund, and through the State’s Growing 

Greener Program. 

Pennsylvania’s definition of a “significant lake” is a waterbody with public access and a 

hydraulic residence time of 14 days or more. Pennsylvania currently has 223 verified significant 

lakes totaling 126,867 acres. Another 156 public waterways are used as lakes but may not have 

the 14-day retention time. Lake assessments are done on “significant” lakes and other lakes by 

DEP and various partners including USGS, SRBC, EPA, other state agencies (Department of 

Conservation and Natural Resources, DCNR), citizen volunteers, County Conservation Districts, 

Morris Arboretum, and consultants. Currently 252 lakes have current use- assessment data 

(within 10 years or less) from which the Integrated Report is developed. Lakes assessed through 

2011 are included in this Report. 

Lake data from the above efforts are reviewed to evaluate support of designated uses and 

compliance with water quality criteria. Updated DEP lake assessment methodologies have been 

publicly reviewed and are posted on DEP’s Water Quality webpage at 

http://www.portal.state.pa.us/portal/server.pt/community/water_quality_standards/10556/2009_a

ssessment_methodology/666876. 

Lake impairment screening to determine the TSI, identify water quality violations and determine 

impacts on recreational uses and aquatic life is ongoing statewide. TSI lake survey results, along 

with other water chemistry parameters, fish and aquatic macrophyte survey data, lake habitat 

surveys, and microbiological data (bacteria, algal and cyanotoxin data) are used to determine 

lake use attainment status. These studies also identify waterbodies in need of more in-depth 

(Clean Lakes Phase I type) studies that would evaluate existing water quality conditions in the 

lake and watershed, identify sources and magnitude of pollutants, and recommend lake and 

watershed management plans to restore or protect water quality. Phase II projects continue 

documentation of water quality conditions and also implement lake and watershed BMPs as 

recommended in the Phase I management plan.
29

Institutional BMPs, (environmental education efforts, such as workshops and outreach), are 

integral components of successful projects and can be as important as structural BMPs. 

Continued water quality studies are recommended to monitor the success of control efforts. Also, 

TMDL lakes are targeted for monitoring on a continuing basis, post BMP installation, so that 

water quality improvements may be detected and reported. Several of the TMDL lakes are 

improving and have been subjects of “Success Stories” (DEP website: 

http://www.portal.state.pa.us/portal/server.pt/community/nonpoint_source_management/10615/s

uccess_stories/554277 and EPA’s “Success Stories” featured on their website: 

http://water.epa.gov/polwaste/nps/success319/.

 

Lake acreages herein are standardized to the acres reported in the National Hydrography Data set 

(NHD) where possible. Some differences in reported acreages will remain until all data are 

extracted from only the NHD layer and errors in the NHD layer are corrected. Until all the lake 

data can be entered and retrieved from the ICE computer application, lake numbers reported for 

various statistics and tables will be variable. 

Part C1.6. Citizens’ Volunteer Monitoring

In July 2009, due to budget constraints, DEP began limiting its direct technical and financial 

support for volunteer monitors to specific projects that result in the generation of quality assured 

data related to DEP’s highest priorities. Projects related to DEP’s priorities include working 

with program staff and volunteers to monitor sections of streams to assess impacts from stream 

restoration projects, best management practices and abandoned mine land remediation projects, 

which are supported by 319 Non-point Source Program or DEP monies. Conservation Reserve 

Enhancement Program (CREP) activities are also being monitored to assess the effectiveness of 

these practices. As priorities change and needs arise, DEP will continue to work with volunteers 

in monitoring the effectiveness of projects.

Requests from volunteer monitors for services previously provided by DEP such as routine 

technical assistance and training on preparation and implementation of a locally driven 

monitoring plan are being directed to the Consortium for Scientific Assistance to Watersheds or 

Nature Abounds. The Consortium, a group of service providers, is funded through a Growing 

Greener grant administered by DEP while Nature Abounds, a nonprofit organization, has a 319 

Non-point Source Management grant to support the Pennsylvania Senior Environment Corps 

program and monitoring.

Part C1.7. Existing and Readily Available Information

In an effort to utilize all existing and readily available data, DEP contacted about 500 potential 

outside data sources (federal, state, and local governments; universities; advisory groups; citizen 

monitoring groups; watershed associations; public interest groups; and sportsmen’s groups) to 

request information regarding water quality. Each group on the mailing list received materials 

that briefly explained the reasons why DEP was soliciting information from them. Minimum 

quality assurance standards for the data were made available on DEP’s website. Those groups 

with data and/or information regarding water quality limited segments were requested to fill out 
30

a data submission form and return it, along with any pertinent supporting documentation, to 

DEP.

For any given listing cycle, DEP determines the accuracy and validity of existing and readily 

available data and information provided by outside groups based on a set of minimum quality 

assurance requirements. These requirements include the specific location of the reported 

impairment, identification of the particular water quality standards violation(s), data to 

substantiate the conclusion of impairment, identification of the source(s) and cause(s) of 

impairment, and the presence of a quality assurance/quality control plan. Acceptable data from 

these sources are then included in the assessment database to prepare the use support summary in

this narrative report and the five-part list of waterbody-specific use support decisions. More 

detail on this process is provided in the assessment and listing methodology document associated 

with the five-part list.

Data from four separate outside data sources were submitted to DEP for consideration in the 

2012 Integrated Report. The Chester Water Authority submitted coliform and nitrate plus nitrite 

data for the Octoraro Reservoir and nitrate plus nitrite data for the East and West Branches of 

Octoraro Creek. The East and West Branches of Octoraro Creek were placed on List 5 of the 

Integrated Report in 2006, with a cause of nutrients. The data submitted this year confirms the 

continued impairment of the Potable Water Supply use.

The Chester Ridley Crum (CRC) Volunteer Monitoring program submitted water chemistry data 

for Goose Creek, East and West Branches of Chester Creek, Ridley Creek, Chester Creek, and 

Little Crum Creek. For each station, those parameters that DEP has a water quality criterion for 

were analyzed. The majority of parameters did not exceed DEP criteria. Many of the stations 

did have temperature exceedances, however, DEP temperature criteria is to be applied to waters 

receiving thermal discharges, which were absent from the surveyed sections of Ridley Creek. In 

addition, Ridley Creek was assessed by DEP biologists in 2011 and found to be impaired for its 

aquatic life use. 

The Pennsylvania Fish and Boat Commission (PFBC) in conjunction with four other 

organizations submitted pH and dissolved oxygen (D.O.) data for the Susquehanna River. Realtime data was collected every 30 minutes starting in May 2008 and ending in the fall of 2009 for 

two sites and in fall 2010 for the third site. Although the data showed some exceedance of DO 

and pH criteria at times, they were not sufficient to warrant an impaired listing for the identified 

river reach. 

DEP works with Department of Conservation and Natural Resources (DCNR) and the state 

Department of Health (DOH) to obtain Escherichia coli results for beach monitoring at state park 

and private beaches, respectively. Information obtained from the agencies is utilized to target 

sampling efforts by DEP for fecal coliforms the following bathing season. Beaches monitored 

by DEP for fecal coliforms are then assessed for recreational use attainment. No beaches 

monitored by DCNR in 2010 and 2011 were targeted by DEP to be included in the 2012 

Integrated Report.

The Citizen Volunteer Monitoring Program and the Division of Water Quality Standards 

solicited volunteers across the state for bacteria sampling. Volunteers from Senior 

Environmental Corps (SEC), Watershed Associations, County Conservation Districts and 

Delaware River Basin Commission (DRBC) staff were trained by DEP in adherence to sampling 
31

protocol and quality/assurance plans to ensure data collected would be usable for recreational use 

assessments. Twenty-four SECs and Watershed Associations, ten County Conservation 

Districts, and Department personnel participated in the collection of fecal coliform samples at 

126 sites on eighty-five streams. DRBC sampled an additional thirteen sites on seven streams. 

Data submitted from the various groups resulted in thirty-five stream attainments and forty-five 

stream impairments for recreation.

Part C2.1: Assessment and Methodology

Because of its length, the 2009 Assessment Methodology is not included with this report but 

rather is posted separately on DEP’s website. It is available electronically at 

www.dep.state.pa.us. Use the following keywords: Water, Water Quality, and, finally, 2009

Assessment Methodology.

The Methodology describes the collection and analytical methods used to evaluate stream 

assessment information. The resulting assessments comprise the stream miles, lake acreages, and 

attained/impaired status reported in the 2012 Integrated Report. 

The 2009 Assessment Methodology contains the following protocols:

Watershed Assessments

Instream Comprehensive Evaluations (ICE)

Macroinvertebrate Stream Protocols

Limestone Streams

Multi-Habitat (Pool/Glide Streams)

Riffle/Run Freestone Streams

Lake Protocols

Lake Assessment

Aquatic Macrophyte Coverage Procedures for Lake Assessments

Lake Fisheries

Evaluation of Phosphorous Discharges to Lakes, Ponds, and Impoundments

Plankton Sampling

Chlorophyll A Sampling

Chemistry and Bacteria

Chemistry Evaluations

Fish Tissue Sampling

Bacterial Sampling

Natural Sources

Natural Pollutant Sources

Outside Agency

Outside Agency Data

Appendices

Appendix A – Source and Cause Definitions
32

Appendix B – Taxa Tolerance Values

Part C3.1. Stream Use Support

Table 2 is a summary of the four use support categories used in listing. Miles “supporting” are 

the number of miles not impaired for an assessed water use; “impaired” are not supporting the 

assessed use and requiring a TMDL; “approved TMDL” refers to impaired segments for which 

an approved TMDL is in place to address the problem(s), and “compliance” lists steam miles 

impaired but expected to improve in a reasonable amount of time because formal agreements are 

in place obligating responsible parties to take corrective action. “Pollution” is a special category 

of impairment listing problems that cannot be addressed through a TMDL because they are not 

caused by pollutant loading. “Assessed” represents the total miles surveyed for that use. 

Table 3 summarizes the sources of impairment problems and Table 4 the causes. Note that 

totaling the sources or causes will not equal the miles summarized in Table 2 because a given 

waterbody may have multiple sources and/or causes. The tables are statewide summaries. Table 

4 has been modified since the 2010 Integrated Report to clarify the causes of 

Salinity/TDS/Chlorides. Salinity and Chlorides were removed from the grouping as none of the 

previous and current impairments were attributed to these 2 causes, as all were impaired solely 

by TDS. The individual source/cause pairs for each waterbody are found on Categories 5, 4b, 

and 4c. The lists are large and, as a result, are provided separately in electronic format. 

Table 2

Statewide Assessment Summary

A statewide summary of use support status for four water uses in assessed streams

Aquatic Life 

Use

Fish 

Consumption Use

Recreational 

Use

Potable Water 

Supply Use

Streams (miles)

Assessed 84,571 5,345 2,422 3,357

Supporting 67,972 3,323 1,205 3,194

Impaired 9,801 1,318 1,209 151

*Approved TMDL 6,490 704 8 12

Compliance 62 --- --- ---

**Pollution 2,709 --- --- ---

* TMDL miles reported here are only those overlapping impaired segments. A TMDL allocation 

may include an entire watershed, including streams listed as attained. 

** 1,755 miles have both pollution and pollutant problems
33

Table 3

Statewide Assessment Summary

Sources of Impairment: Streams

Totals Include List 4a, 4b, 4c, and 5

(Mile totals will not equal Table 2 because a waterbody can have multiple impairments)

Designated Use (Miles)

Source Aquatic Life

Fish 

Consumption Recreation

Water 

Supply Total

Agriculture 5,603 65 37 5,705

Abandoned Mine Drainage 5,517 79 5,596

Source Unknown 502 1819 1120 41 3,482

Urban Runoff/Storm Sewers 2,410 41 2,451

Road Runoff 904 904

Small Residential Runoff 748 748

Habitat Modification 629 629

Atmospheric Deposition 483 483

Removal of Vegetation 418 418

Municipal Point Source 380 7 1 388

Channelization 338 338

Bank Modifications 322 322

Other 304 10 314

Land Development 232 232

Industrial Point Source 113 29 67 208

On site Wastewater 199 6 205

Erosion from Derelict Land 192 192

Subsurface Mining 114 67 181

Construction 162 162

Upstream Impoundment 160 160

Natural Sources 152 152

Hydromodification 147 147

Combined Sewer Overflow 19 12 121

Flow Regulation/Modification 119 119

Surface Mining 117 117

Petroleum Activities 60 60
34

Designated Use (Miles)

Source Aquatic Life

Fish 

Consumption Recreation

Water 

Supply Total

Golf Courses 55 55

Silviculture 19 19

Highway, Road, Bridge Const. 16 16

Package Plants 15 15

Land Disposal 13 13

Draining or Filling 10 10

Recreation and Tourism 3 3

Logging Roads 2 2

Dredging 1 1
35

Table 4

Statewide Assessment Summary

Cause of Impairment: Streams

Totals Include List 4a, 4b, 4c, and 5

(Mile totals will not equal Table 2 because a waterbody can have multiple impairments)

Use Designation (Miles)

Cause

Aquatic 

Life

Fish 

Consumption Recreation

Water 

Supply Total

Siltation 8,712 2 8,714

Metals 5,031 12 5,043

pH 2,847 2,847

Nutrients 2,615 34 2,649

Water/Flow Variability 1,559 1,559

Organic Enrichment/Low D.O. 1,309 1,309

Pathogens 1,227 39 1,266

Cause Unknown 1,137 3 1,140

Mercury 1,076 1,076

Other Habitat Alterations 997 997

PCB 968 968

Flow Alterations 708 708

Suspended Solids 538 538

Turbidity 227 227

Excessive Algal Growth 128 128

Other Inorganics 51 71 122

TDS* 98 . 8 106

Thermal Modifications 85 85

Chlordane 84 84

Unknown Toxicity 68 68

Dioxins 46 46

Oil and Grease 40 40

Osmotic Pressure 34 34

Exotic Species 31 31

Pesticides 23 23

Nonpriority Organics 23 23
36

Use Designation (Miles)

Cause

Aquatic 

Life

Fish 

Consumption Recreation

Water 

Supply Total

Priority Organics 21 21

DO/BOD temp 20 20

Unionized Ammonia 18 18

Chlorine 9 9

Filling and Draining 6 6

Trash 1 1

* Was Salinity/TDS/Chlorides in previous Integrated Reports. Revision reflects actual cause of impairments.

Monitoring information indicates that 67,972 miles support designated aquatic life use. A total 

of 9,801 miles are reported as impaired and still requiring a TMDL and 6,490 miles are impaired 

but already have an approved TMDL. There are 2,709 miles with pollution problems not 

requiring a TMDL and 62 miles are impaired but expected to improve in a reasonable time 

pending agreed upon corrective action. 

The three largest known sources of reported impairment for aquatic life are abandoned mine 

drainage, agriculture, and urban runoff/storm sewers. The leading causes are siltation, metals, 

pH, nutrients, water/flow variability, and organic/enrichment. While direct source/cause

linkages cannot be made at the level of detail presented in Tables 3 and 4, causes other than 

water/flow variability are known to be associated with the three leading sources of abandoned 

mine drainage, agriculture, and urban runoff/storm sewers. Agricultural impairments are 

generally caused by nutrients and siltation associated with surface runoff, groundwater input and 

unrestricted access of livestock to streams. Low pH, elevated concentrations of metals, and 

siltation are the result of abandoned mine drainage runoff from mine lands and refuse piles. 

Increased levels of nutrients and siltation, along with flow variability, are associated with urban 

runoff. The sources associated with water/flow variability are varied, including 

hydromodification, road runoff, urban runoff/storm sewers, and several others. Any source that 

alters runoff or stream flow can affect water/flow variability. Water/flow variability is 

considered pollution not requiring a TMDL but the problem still requires remediation.

There are 3,323 assessed miles supporting the fish consumption use and 1,318 miles impaired 

and still requiring a TMDL. There are approved TMDLs for 704 miles. The 3,323 miles 

supporting this use is a conservative estimate. As a rule, when fish tissue samples are clean the 

results are only extrapolated to represent two miles on small streams and ten on larger 

waterbodies. To protect the public, larger extrapolations are made when the fish tissue samples 

are tainted. 

The major source of contamination resulting in fish consumption advisories is listed as unknown 

because it is difficult to trace the sources. The contamination can be in the soil, groundwater, 

stream sediment, or point sources. The contaminants do not readily break down and can linger 

for decades. In addition, fish can move considerable distances. Only with careful study can the 

source of contamination be determined with certainty. The contaminants documented are PCB, 

mercury, chlordane, and dioxin in decreasing order. Atmospheric deposition is the most likely 

source of the mercury. There is a statewide advisory limiting consumption of recreationally 
37

caught fish to one meal per week. If fish tissue mercury concentrations are greater than the one 

meal per week level (higher concentrations), they are placed on Category 5 of waters. 

Conversely, if subsequent samples indicate the concentrations are now less than the one meal per 

week level they are removed from Category 5. 

Recreational use is assessed primarily by measuring bacteria levels. High bacteria densities 

indicate conditions that might cause sickness from contact with or ingestion of the water. Many 

of the waters targeted for sampling were suspected of having bacteria problems so the 1,209

miles of impaired miles versus the 1,205 miles attaining is not unexpected. There are 8 miles 

with an approved pathogen TMDL. The major source of pathogens is listed as source unknown 

followed by agriculture. If there are several potential sources of bacteria in the watershed the 

assessor lists the source as unknown until better information becomes available. 

Potable water supply use was supported in 3,194 miles of streams assessed, not supported in 151, 

and 12 had approved TMDLs. This potable water supply use is measured before the water is 

treated for consumption. The primary assessment measures are nitrate and nitrite levels and 

bacteria but additional parameters, both organic and inorganic, are considered. 

Part C3.2. Record of changes to the 2010 Integrated List 5 made in the 2012 Integrated List

The Integrated List is part of a biennial report. The previous list included data gathered through 

2009. In the two year period leading up to this report, a number of waterbodies listed as impaired 

on the 2010 Integrated Report were resurveyed. Impaired waters may be resurveyed for a 

number of reasons including the need for additional data to support TMDL development, or 

changes in land use, or point source discharge characteristics. Waters are revaluated on a 

rotating basis as per the ICE sampling protocol outlined in the 2009 Assessment Methodology. 

Areas where watershed improvement projects are in place are also targeted to document 

improvements that may results. 

Appendix E tracks changes in the status of waters impaired in 2010 but attaining uses in 2012. 

Each of these delistings is the result of a detailed chemical or biological survey and subsequent 

data evaluation. Appendix F tracks changes in the pollutant causes. Entries for waters that were 

reported as impaired in 2010 but, subsequent surveys found them to be impaired but by different 

pollutants, are edited to better reflect the problems. The comments associated with each record 

describe the changes. Lastly, Appendix G describes records with errors. Some are mapping 

errors discovered because the GIS coverage has undergone several revisions over the past 14

years and occasionally some legacy mapping errors are uncovered. Other errors relate to an 

impairment being incorrectly mapped to a pollutant source. Comments in these records describe 

the error. 

Part C3.3. Lakes Use Support

Table 5 is a summary of the four use support categories for lakes. Acres “supporting” is the 

number of acres not impaired for the assessed use. “Impaired” acres (List 5) do not support the 

assessed use and still require a TMDL. “Approved TMDL” includes impaired lake waters where 

a TMDL has been completed and approved by EPA. ”Impaired (List 4c)” is a special category of 

use impairment where a problem is documented but it will not be addressed through a TMDL. 

Pollution is a special category of impairment where there is a problem but it will not be 
38

addressed through a TMDL because it does not involve pollutant loadings. “Assessed” refers to 

the total acres surveyed for that use. 

Table 6 summarizes the sources of impairment problems and Table 7 the causes. Note that 

totaling the sources or causes will not equal the acres summarized in Table 5. This is because a 

waterbody may have multiple sources and causes. The individual source/cause pairs for each 

waterbody are found on List 5, 4b, and 4c. The lists are large and as a result are presented only in 

electronic format separate from this narrative. 

Table 5

Statewide Lake Assessment Summary

A statewide summary of use support status for four water uses in assessed lakes

Aquatic 

Life Use

Fish 

Consumption 

Use

Recreational 

Use

Potable Water 

Supply Use

Lakes (acres)

Assessed 80,525 74,835 81,959 58,013

Supporting (Lists 1 & 2) 43,194 28,765 76,836 57,941

Impaired (List 5) 5,420 40,405 5,123 12

Impaired (List 4c) 20,544 --- --- ---

Approved TMDL List 

4a

11,366* 5,664 --- ---

* Lake Jean pH TMDL (248 acres) now attaining, so no longer included in TMDL total.

* Dutch Fork Lake (87 acres) has a completed TMDL but has been breached so is no longer

impaired; however PFBC is reconstructing the impoundment.

* Presque Isle Bay acres are included in the fish consumption and recreation use totals. The 

remainder of Lake Erie is not included in the pathogen and recreation acre totals. 

Pennsylvania has 63 miles of Lake Erie shoreline, 14 of which comprise Presque Isle.
39

Table 6

Statewide Assessment Summary

Sources of Impairment: Lakes

Totals Include List 4a, 4b, 4c, and 5

(Acre totals will not equal Table 5 because a waterbody can have multiple impairments)

Use Designation (Acres)

Source

Aquatic 

Life

Fish 

Consumption Recreation

Water 

Supply Total

Atmospheric Deposition 219 32,174 32,393

Source Unknown 2,921 13,896 3,718 20,535

Other 20,019 20,019

Agriculture 13,006 1,307 14,313

Urban Runoff/Storm Sewers 3,628 82 3,710

On site Wastewater 3,223 87 3,310

Municipal Point Source 2,439 2,439

Natural Sources 1,222 1,222

Habitat Modification 486 68 554

Small Residential Runoff 531 531

Removal of Vegetation 445 445

Abandoned Mine Drainage 365 12 377

Golf Courses 210 210

Bank Modification 192 192

Road Runoff 185 5 190

Recreation and Tourism 185 185

Package Plants 160 160

Hydromodification 121 121

Construction 76 76

Land Development 5 5 10
40

Table 7

Statewide Assessment Summary

Causes of Impairment: Lakes

Totals Include List 4a, 4b, 4c, and 5

(Acre totals will not equal Table 5 because a waterbody can have multiple impairments)

Use Designation (Acres)

Cause Aquatic Life

Fish 

Consumption Recreation

Water 

Supply Total

Mercury (Lakes) 39,580 39,580

pH 15,852 15,852

Nutrients 13,954 137 13,731

Suspended Solids 10,976 57 11,033

Organic Enrichment/Low 

D.O. 8,603 8,603

Pathogens 4,897 4,897

PCB 3,921 3,921

DO/BOD 1,280 1,280

Excessive Algal Growth 471 31 502

Turbidity 445 445

Metals 365 12 377

Exotic Species 226 77 303

Siltation 255 46 301

Noxious Aquatic Plants 291 5 296

Other Habitat Alterations 31 31

Unionized Ammonia 25 25

A total of 80,525 acres of Commonwealth lakes have been assessed for aquatic life use and of 

these acres, 43,194 acres support that use. There are 5,420 assessed lake acres that are impaired 

and still require a TMDL. Approved TMDLs are in place for 11,366 acres. Pollution problems 

that do not require TMDLs impair 20,544 acres. The major sources of aquatic life use 

impairment in lakes are “other”, and agriculture. “Other” is the source used for lakes on List 4c 

which are impaired but not requiring a TMDL. These lakes show short term fluctuations in DO 

or pH but support a healthy fish community. The primary stressors are nutrients, suspended 

solids, organic enrichment/low DO, and pH. Low DO and high pH problems are associated with 

summer lake stratification. 
41

Fish consumption assessments covered 74,835 lake acres (excluding Lake Erie but not Presque 

Isle Bay). Of these, 28,765 acres are assessed as supporting this use, 40,405 acres are reported as 

requiring a TMDL, and 5,664 acres have approved TMDLs. The reason for the large proportion 

of impaired acres is the implementation of Pennsylvania’s risk-based mercury fish consumption 

advisory methodology in 2001. Nearly all of the lake advisories are due to mercury with 

atmospheric deposition listed as the source. 

In addition, fish consumption advisories are in place for a number of species in the Pennsylvania 

portion of Lake Erie. These advisories are due to PCB and mercury. There are 63 miles of Lake 

Erie shoreline in Pennsylvania fourteen of which comprise the Presque Isle Peninsula. 

A total of 81,959 lake acres have been assessed for recreation use support and 5,123 of those 

acres require TMDLs. Pathogens and nutrients from agriculture and on site wastewater are 

responsible for the impairments.

All but 12 acres of 58,013 acres assessed for potable water supply use were found to be attaining 

that use.

Part C3.4. Excluding the Fishable and Swimmable Uses

DEP routinely re-evaluates, as part of its triennial review of water quality standards, the two 

water bodies where the fishable or swimmable uses specified in Section 101(a) (2) of the federal 

Clean Water Act are not being met: (1) the Harbor Basin and entrance channel to Outer Erie 

Harbor/ Presque Isle Bay and (2) several zones in the Delaware Estuary.

The swimmable use designation was deleted from the Harbor Basin and entrance channel 

demarcated by U.S. Coast Guard buoys and channel markers on Outer Erie Harbor/ Presque Isle 

Bay because boat and commercial shipping traffic pose a serious safety hazard in this area. This 

decision was based on a Use Attainability study completed in 1985. Because the same 

conditions and hazards exist today, no change to the designated use for Outer Erie Harbor/ 

Presque Isle Bay is proposed.

DEP cooperated with the Delaware River Basin Commission (DRBC), EPA and other DRBC 

signatory states on a comprehensive Use Attainability study in the lower Delaware River and 

Delaware Estuary. This study resulted in appropriate restrictions relating to the swimmable use, 

which DRBC included in water use classifications and water quality criteria for portions of the 

tidal Delaware River in May 1991. These changes were incorporated into Sections 93.9e and 

93.9g (Drainage Lists E and G) of Pennsylvania’s Water Quality Standards in 1994. The 

primary water contact use remains excluded from the designated uses for river miles 108.4 to 

81.8 because of continuing significant impacts from combined sewer overflows and other 

hazards, such as commercial shipping traffic.

Part C3.5. Lakes Trophic Status

Lake trophic status, based on Carlson's Trophic State Index (TSI), is used as a tool to monitor 

lake status in Pennsylvania. Lakes with a TSI of less than 40 are oligotrophic (nutrient poor); 40-

50 is mesotrophic; 50-65 is eutrophic (nutrient rich); and greater than 65 TSI is considered 
42

hypereutrophic. TSIs for Pennsylvania lakes are based on seasonal mean values of phosphorus, 

secchi depth and chlorophyll a. See Methods documents cited above). Trophic category is based 

on the Total Phosphorus (TP) TSI. Table 8 summarizes lake trophic status. Sums do not include 

Lake Erie, but do include Presque Isle Bay for pertinent data. 

Table 8

Lake Trophic Status: Summary of Lakes Assessed

Number of Lakes Acreage of Lakes

Total Assessed (all types) 495

Assessed for TSI (2001 to current) 252 77,071.8*

Oligotrophic 16 3,258.0

Mesotrophic 102 32,787.4

Eutrophic 96 20,608.1

Hypereutrophic 13 18,702.0

Unassigned (data not assembled or current 

WQNs)

25 1,716.3

* Excel summary table calculation, not NHD coverage. 

Part C3.6. Lake Restoration Efforts

The Commonwealth's lake protection and restoration program is mainly supported by EPA's 

Nonpoint Source Program (Section 319 of the Clean Water Act) and the state's Environmental 

Stewardship Program, through Growing Greener grants. Other funding sources include EPA 

Section 104(b)3 grants, the Natural Resources Conservation Service (NRCS) PL566 program, 

and other programs such as the Chesapeake Bay Program and PENNVEST (Clean Water State 

Revolving Funds). DCNR also funds in-lake restoration practices for State Park lakes. Various 

partners are engaged in lake and lake watershed restorations, and are not limited to the lake 

owners. Watershed partners include county Conservation Districts which implement many DEP 

program initiatives and also serve as grant and project managers. Program goals to restore and/or 

protect lake water quality are based on studies that identify impairments, pollution sources and 

the course of remediation. Public use and benefit of the lake, and watershed priority based on 

impairment are important criteria in prioritizing lakes to be funded.

Restoration techniques implemented through Phase II or restoration grants include various 

watershed and in-lake best management practices (BMPs) such as agricultural BMPs, riparian 

corridor protection and restoration (buffers and in-stream structures), lake shoreline protection, 

dredging, stormwater management and control techniques, point source controls, aquatic 

macrophyte controls, lake and watershed liming, alum treatments, biomanipulation to benefit 

fisheries, lake drawdowns, septic management, wildlife control, and institutional BMPs such as 

public education efforts and enacting protective municipal ordinances. Sewage treatment plant 

upgrades are also an important control technique to improve lake water quality. Invasive species 

are also an important restoration theme, with increasing numbers of lakes impacted by Eurasian 

watermilfoil, water chestnut, and zebra/quaaga mussels. Some limited Growing Greener and Sea 

Grant funds are available for control of these organisms. 
43

Table 9 provides information on current Phase I (assessments) and Phase II 

(restoration/implementation) lake work being conducted in the Commonwealth. Expenditures on 

active lake projects or lake watershed projects in Pennsylvania currently amounts to 

approximately $4.3 million for projects current through 2011. Table 10 summarizes known 

techniques used in lake restoration projects in Pennsylvania’s public lakes.

Part C3.7. Lake Control Methods

Pennsylvania's lake management regulation is codified in DEP's Rules and Regulations at 

Section 96.5 - Discharges to Lakes, Ponds and Impoundments, which sets forth treatment 

requirements for point source discharges necessary to control eutrophication. It is a technologybased approach that results in increasingly stringent effluent requirements based on an 

assessment of the water quality benefits of such controls. The need for and extent of point 

source controls for a specific lake are determined by field studies conducted during spring 

overturn, summer stratification and fall overturn. Appropriate nutrient limitations and 

monitoring requirements are included in NPDES permits based on the trophic conditions found 

during these studies. In most cases, follow-up monitoring is conducted to evaluate the adequacy 

of the effluent limitations.

Nonpoint source pollution can also impact lake water quality. Phase I diagnostic studies on 

Pennsylvania lakes have identified nonpoint source impacts from acid deposition, agricultural 

runoff, streambank erosion, malfunctioning septic systems, construction, stormwater runoff, and 

pathogens. Mitigation of these sources is highlighted in the previous section. Acidity problems, 

resulting mostly from acid deposition, but also in a few cases mining runoff, may be mitigated 

with lime treatments, although funding for these types of projects is very limited. Lakes with 

naturally low pH (swamps and bogs) are not considered for treatment, but may be listed on part 

4C of the Integrated List. Liming is the current method to mitigate low pH in lakes, and is used 

in PA on both public and private lakes. Some lakes (reservoirs) have been identified as impaired 

by metals from mine drainage, or more commonly by mercury (mainly via fish tissue) and none 

have been identified as impacted by “high acidity,” based on high concentrations of dissolved 

metals. Restoration efforts and BMPs in the watershed are the best way to reduce mining effects 

in waterbodies (i.e. treating the source of the problem). In-lake mitigation could be explored by 

using alum treatments to bind metals into the lake sediments. Some “toxics” can be removed by 

dredging but again, funding for dredging is limited. Most efforts have focused on source control 

(mining BMPs or AMD BMPs) and natural recovery rather than in-lake mitigation.
44

Table 9. Active Lake Projects in Pennsylvania Public Lakes as of 2011. Does not include water quality assessments done by DEP. 

Growing Greener and 319 final reports available from DEP, Bureau of Conservation and Restoration.

Lake or Study 

Name County Study Type

Study 

Period

Federal 

Funds

Fund 

Source State Funds 319 Funds Match Sponsor /Project

Antiedam Lake Berks Phase II 2010-2012 GG $145,000 $21,750 

Berks Co 

Commissioners; 

stream BMPs

Bald Eagle Lake Centre Phase III 2007-2012 GG $150,000 $39,200 Centre CCD; stream 

BMPs (partial applied 

to this watershed) 

Blue Marsh Lake Berks Phase II 2010-2012 GG $51,593 $74,322 Berks CCD

Conneaut Lake Crawford

Phase I

2008-2010

GG $35,000 $25,000

Crawford CCD; 

Stormwater Plan

Conneaut Lake Crawford Phase II 2011-2012 GG $2,997 Conneaut School 

District/ EE

Conneaut Lake Crawford Phase II 2010-2012 GG $43,050 $6,458 

Crawford CCD/ ag 

BMPs (partial in lake 

watershed)

C-SAW - Various 

Small Lake 

Projects

multi Phase I 2010-2012 GG $300,000 $161,114 

C-SAW - Consortium 

of Scientif Assistance 

to Watersheds

Frances Slocum 

Lake Luzerne Phase I 2007-2011 $48,900 319 Luzerne CCD; WIP

Frances Slocum 

Lake Luzerne Phase I 2009-2010 $48,900 319 $48,900

Luzerne CCD, 

Watershed 

Implementation Plan

Foster Joseph 

Sayres Centre Phase II 2010-2012 GG $37,778 $61,004 

Clearwater 

Conservancy; 

watershed BMPs
45

Lake or Study 

Name County Study Type

Study 

Period

Federal 

Funds

Fund 

Source State Funds 319 Funds Match Sponsor /Project

Glendale Lake Cambria Phase II 2008-2011 GG $43,500 $13,106 Cambria CCD

Greenlick 

Reservoir Fayette Phase II 2010-2012 GG $10,000 $1,500 

Jacobs Creek 

Watershed Assn; 

shoreline stabilization

Harveys Lake Luzerne Phase II 

and III 2009-2012 $262,534 319 $262,534 $48,315 Harveys Lake Borough;

Harveys Lake Luzerne Phase II 

and III 2010-2012 $565,700 319 $565,700 $100,000 stormwater BMPs and monitoring

Lake Carey Woming Phase II 2008-2012 GG $308,939 $67,490 

Lake Carey Welfare 

Association; 

stormwater BMPs

Lake Erie Erie Phase II 2009-2012 $247,825 319 $247,825 $37,000 Erie CCD; stream, Ag, 

and EE BMPs

Lake Erie Erie Phase I 2007-2012 GG $20,000 $117,984 Erie CCD; develop a 

plan for Trout Run

Lake Erie Erie Phase II 2008-2012 $150,000 319 $150,000 $32,800 Erie CCD; Trout Run 

BMPs

Lake Erie Erie Phase II 2008-2012 GG $35,000 $65,000 Erie CCD; septic 

system BMPs

Lake Erie Erie Phase II 2008-2012 GG $200,000 $120,926 Erie CCD; Cascade 

Creek stream BMPs

Lake Erie Erie Phase II 2008-2012 GG $13,785 $91,900 

Erie PSU; stream 

projects & monitoring 

Bear Run

Lake Galena Bucks Phase II 2011-2012

(part of 

PALMS 

below)

GG, 

PALMS

Bucks CCD/ lakeshore 

restoration
46

Lake or Study 

Name County Study Type

Study 

Period

Federal 

Funds

Fund 

Source State Funds 319 Funds Match Sponsor /Project

Lake Jean Luzerne, 

Sullivan Phase II 1995-yearly DCNR $1,500 Bureau of State Parks/ liming

Lake Pleasant Erie Phase II 2011-2012

(part of 

PALMS 

below)

GG, 

PALMS

Western PA 

Conservancy; invasive 

control

Lakes Redman 

and Williams York Phase II 2008-2011 GG $100,000 $65,110 

York Watershed 

Alliance ; stream 

stabalization

Lake 

Wallenpaupack

Pike, 

Wayne Phase II 2008-2010 GG $40,530 $10,133

Lake Wallenpaupack 

Watershed 

Management District; 

farm BMPs

Lake Wilhelm Mercer Phase II 2011-2012

(part of 

PALMS 

below)

GG, 

PALMS DCNR

Laurel Hill Lake 

and Kooser Lake Somerset Phase I 2008-2012 GG $30,900 $14,958 Somerset CCD; 

watershed assessment

Laurel Hill Lake 

and Kooser Lake Somerset Phase I 2008-2012 GG $240,240 $108,097 Somerset CCD; flow 

and sediment analysis

Magnolia Lake Bucks Phase II 2009-2012 GG $44,341 $8,770 Bucks CCD; lakeshore 

stabilization

North Fork Dam Potter Phase II 2009-2012 GG $23,306 $33,634 Potter Co. 

Commissioners

Ontelaunee Lake Berks Phase II 2009-2012 GG $90,435 $25,300 Berks CCD; ag BMPs

PA Lake 

Management 

Socety (PALMS)

multi Phase I 

and II 2009-2012 GG $250,000 $37,500 various lake projects statewide
47

Lake or Study 

Name County Study Type

Study 

Period

Federal 

Funds

Fund 

Source State Funds 319 Funds Match Sponsor /Project

Shenango Res. 

(watershed) Mercer Phase II 2008-2012 GG $18,709 $8,000 

Shenango River 

Watchers; bank 

stabilization

Somerset Lake Chester Phase I 2010-2012 GG $39,835 $7,675 New Garden Twp. 

Stephen Foster 

Lake Bradford Phase II 2007-2011 $194,468 319 $194,468 

Bradford 

CCD/Watershed and 

In-lake BMPs

Stephen Foster 

Lake Bradford Phase III 2010-2012 $6,000 319 $6,000 Efficacy monitoring

Stephen Foster 

Lake Bradford Phase II 2010-2012 $161,938 319 $161,938 $28,390 Mill Creek streambank restoration

Stephen Foster 

Lake Bradford Phase II 2011-2012 $1,000 319 $1,000 Education Mini-grant

Tioga Lake Tioga Phase II 2009-2012 GG $175,000 $104,000 Tioga CCD; ag BMPs

Tioga Lake 

Tioga Phase II 2008-2012 GG $227,107 $34,066

Tioga CCD; Dirt & 

Gravel Roads

Total Funds $1,687,265 $2,678,545 $1,638,365 $1,570,502 

Total Federal and 

State Funds $4,365,810 

319 = Nonpoint Source Program

DCNR = PA Dept. Conservation & Natural Resources

GG = Growing Greener Program, PA Environmental Stewardship Funds

CCD = County Conservation District

Phase 1 = lake & watershed assessment/monitoring & management plan

Phase II = restoration BMPs, including Educational

Phase III = monitoring for efficacy, post-TMDL
48

Table 10

Lake Rehabilitation Techniques Used in Public Lakes

Technique

Number of Lakes 

Where Technique 

Used

Acres of Lakes Where

Technique Used

In-Lake Treatment

Aeration 4 120

Aquatic herbicide treatment 40 422

Aquatic macrophyte harvesting 4 60

Lake drawdowns 22 7,285

Liming 1 100

Watershed Treatments

Sediment traps/detention basins 7 8,203

Shoreline erosion controls/bank stabilization 12 14,051

Conservation tillage 4 7,633

Animal waste management practices installed 7 9,787

Riprap installed 4 7,334

Road or skid trail management 4 14,654

Stream restoration (natural channel design) 3 1665

Created wetlands 5 1794

Other Lake Protection/Restoration Controls

Local lake management program in place 22 15,207

Public information/education program/activities 55 63,019

Local ordinances/regulations to protect lake 3 6,600

Point source controls 16 13,888

Part C4. Wetlands Protection Program

Pennsylvania has 403,924 acres of wetlands and 412,905 acres of deep-water habitats such as 

ponds and lakes. About 1.4 percent of the Commonwealth's land surface is represented by 

wetlands, with 97 percent classified as palustrine. Approximately 76 percent of the palustrine 

wetlands are further classified as forested and scrub/shrub wetlands. Lacustrine wetlands, 

mainly composed of the shallow zone (less than 6.6 feet deep) of Lake Erie, represent about two 

percent of the total, while riverine wetlands make up the remaining one percent. Pennsylvania 

has 512 acres of tidal wetlands in the Delaware Estuary.

Wetlands are most abundant in the glaciated portions of northeastern and northwestern 

Pennsylvania. Crawford, Mercer, Erie, Monroe, Pike, Wayne and Luzerne counties contain 40 

percent of the Commonwealth's wetlands. Pike and Monroe counties have the highest 

percentages of land covered by wetlands with 6.7 percent and 6.4 percent, respectively.
49

DEP's authority for the protection of wetlands is primarily established by the Dam Safety and 

Encroachments Act of 1978 and The Clean Streams Law. The Environmental Quality Board 

adopted Chapter 105, Dam Safety and Waterway Management rules and regulations effective 

September 27, 1980. Amended regulations became effective October 12, 1991. Since March 1, 

1995, DEP has been given authority to attach federal Section 404 authorization along with state 

permit approvals for most projects through the Pennsylvania State Programmatic General Permit 

(PASPGP-4). This provides “one-stop shopping” for approximately 80-90 percent of the state 

and federal permit applications received. PASPGP-4 will expire on June 30, 2016. This 

reissuance of the PASPGP-4 included the Mineral Resource program area for the first time as 

eligible to include the federal Section 404 authorization along with the state permit approvals.

Thirty (30) of Pennsylvania's 66 county conservation districts have Chapter 105 Delegation 

Agreements with DEP to register Bureau of Waterways Engineering and Wetlands General 

Permits within their counties. The basic duties of each district are to provide information and 

written materials to the general public on the Dam Safety and Encroachments Act and Chapter 

105 regulations, register general permits, and perform on-site investigations as the first step to 

gain voluntary compliance. In addition to county delegations, program implementation for 

general and individual permit processing and issuance is also delegated to the several DEP 

program areas including the Mineral Resources, Abandon Mine Lands, Conservation and 

Restoration, Oil and Gas and Flood Protection programs. The Office of Water Management 

coordinates this program.

An Environmental Review Committee, consisting of representatives of the U.S. Fish and 

Wildlife Service (USFWS), Pennsylvania Game Commission (PGC), Pennsylvania Fish and 

Boat Commission (PFBC), EPA, U.S. Army Corps of Engineers (ACOE) and DEP, meets 

monthly to review selected applications submitted to DEP. A similar committee has been 

established that meets semi-annually to review ongoing enforcement actions. Through these 

committees, lead agencies are designated for taking action or providing field support to resolve 

violations or to provide data for permit reviews. This coordination economically utilizes limited 

staff of both state and federal agencies.

DEP, in cooperation with the Penn State Cooperative Wetlands Center completed a pilot wetland 

condition assessment in an area of south central Pennsylvania in 2006. The pilot was to test a 

wetland condition assessment methodology that could be expanded to the entire Commonwealth. 

The results from the Level 2 rapid condition assessments have not been statistically analyzed and 

cannot be reported with any confidence intervals nor can the results be projected to the entire 

assessment area. 

Wetlands were separated into four different landcover domains. The land cover domains were 

driven by the percent natural cover (forest and water) and effectively disturbed cover (all types 

of development and barren/mine areas) present within a one kilometer buffer around the 

sampling location. The sample frame population distribution was fairly well distributed based on 

landcover domains.
50

Table 1 Wetland Distribution in Land Cover Domains

Land Cover

Category

Definition Number of

Wetlands

Wetland

Acreage

Entire

Watershed

All wetland points 14,824 36,661.35

Natural Cover > = 65% Natural Cover 

and < 10% EDC

2,828 6,475.89

Non-Forest 

Cover A

< 65% and >35% Natural 

Cover and < 10% EDC

3,372 8,461.78

Non-Forest 

Cover B

< = 35% Natural Cover 

and < 10% EDC

6,605 16,690.34

Effectively 

Disturbed Cover

> = 10% EDC 2,019 5,033.33

The resulting scoring for the 204 sites sampled is depicted in Table1 below. A majority of the 

wetland areas sampled were in a Medium to Low condition category (65% of wetland sample 

areas) which corresponds somewhat with the landcover domain distribution. The Level 2 rapid 

assessment methodology scoring placed a great deal of weight on the Level 1 score, which is 

based upon the percent natural cover located in the one kilometer buffer around the sampling 

area. This resulted in the surrounding landcover being the dominant driver in the Level 2 scoring

Table 2 Level 2 Condition Categories

Condition 

Category

Number of 

Wetlands

Total 

Acreage

Percent of 

Resource

Highest 13 127.74 6.10%

High 59 556.19 26.70%

Medium 41 468.89 22.50%

Low 91 930.07 44.70%

Totals 204 2082.88 100.00%

The stressor category occurrences observed during the Level 2 sampling efforts are depicted in 

Table 3. The Vegetation Alteration, Hydrologic Modification and Sedimentation/ Erosion 

stressor categories were observed most frequently. The most common stressor category 

observed was vegetation alteration. Eighty-eight percent or 180 of the 204 sites sampled 

reported invasive species present. 
51

Table 3. Stressor Occurrence

Stressor Category No of Stressors 

Observed

Acidification 2

Contaminant Toxicity 9

Dissolved Oxygen 2

Eutrophication 4

Hydrologic Modification 58

Sedimentation/Erosion 56

Thermal Alteration 1

Turbidity 2

Vegetation Alteration 150

Total 284

Table 4 shows the breakdown of sites with invasive species and the percent total coverage.

Table 4. Percent occurrence and total cover of invasive species

DEP is the process of completing the study of wetland compensation efforts conducted by 

permittees from 2000-2004, PA Department of Transportation wetland mitigation banks and the 

sites constructed under the in lieu fee program PA Wetland replacement Project. This project 

examined the compliance with regulatory requirements and the effectiveness of compensatory 

mitigation efforts. Part of the findings from this project also resulted in proposed changes to the 

implementation of compensatory mitigation efforts. These program changes are due to occur in 

2012. Chief among the changes are a standard approach for evaluating resource conditions of all 

aquatic resource types and a function based compensatory requirement approach. These 

program changes signify a major shift in how compensatory requirements are determined and 

how they are evaluated.

In 2011, DEP developed a new wetland program plan that addresses program development over 

the next 10 years. One item that was previously drafted in 2009, a wetland monitoring strategy, 

will be finalized in 2012. When completed and publicly participated, the wetland strategy will 

be folded into the PA DEP’s overall comprehensive water quality monitoring strategy. Another 

effort will focus on developing a strategy for establishing a headwater reference population. 

Ultimately, the reference data will be used to build functional models to inform and refine the 

regulatory program efforts for protection and compensation.

No Sites % Total Cover of 

Invasives

% of Sites with 

Invasives

80 0-<5% 39.20%

55 5-20% 26.70%

40 20-50% 19.60%

29 >50% 14.20%

204 100%
52

Part C5. Trend Analysis for Surface Waters

Introduction

Periodically, the Department – assisted greatly by the United States Geological Survey –

analyzes long-term trends of chemical water quality using data collected at fixed-site monitoring 

stations throughout the Commonwealth. Trend analyses were run for two different time frames: 

from October 1, 1991 to September 30, 2010 and from October 1, 2000 to September 2010.

Trend analysis is a statistical technique used to determine if values of a random variable 

generally increase or decrease over some time period. Lack of a trend is good evidence that none 

exists, however there is some possibility that more sample collection will reveal a less obvious 

trend. Conversely, we can be quite confident that changes in water quality are occurring where 

trends are detected.

Methods

The present analyses utilized a parametric trend test developed and performed by United States 

Geologic Survey staff. This approach adjusts observed variation in water quality parameters for 

variation in flow because most water quality parameters exhibit substantial co-variation with 

stream flow. 

Trend tests were run for 18 water quality parameters (Table 1) at a set of 14 water quality 

network (WQN) monitoring stations in areas of the state underlain by Marcellus shale geological 

formations (Figure 1). Most samples in the datasets were collected on a monthly or a bi-monthly 

basis at each station. Trend tests were not run for datasets that had: (1) more than half of the 

data recorded as non-detects; (2) a lot of missing data; or (3) validation issues. Total nitrogen, 

dissolved inorganic phosphorous, total calcium, and total magnesium data were not available 

until 2001 or 2002. Nitrite data were also considered, but most nitrite concentrations were 

reported as below detection limits.

Table 1. Constituents analyzed and abbreviaitons.

Constituent Abbreviation

Total Aluminum Al

Total Copper Cu

Total Iron Fe

Total Lead Pb

Total Zinc Zn

Total Alkalinity ALK

Total Hardness Hard

Total Calcium Ca

Total Magnesium Mg

Total Sulfate SO4

Total Dissolved Solids TDS

Total Ammonia NH4

Nitrate NO3

Total Nitrogen TN

Dissolved Inorganic Phosphorus DIP

Total Phosphorus TP

Total Suspended Solids TSS
53

Figure 1. Locations of the 14 fixed-site, long-term water quality network (WQN) monitroing stations used in the 2012 trend analysis. Major 

waterways (faded blue), major basins (faded black), and county boundaries (faded white) are also shown.
54

Results

Trends for the suite of transition metals (Cu, Zn, Fe) and poor metals (Al, Pb) indicated 

decreasing concentrations for datasets where the trends were statistically significant (Table 2, 

Table 3). Trends for Al were run at six stations in both time frames, and at another four stations 

in the 1991 to 2010 period. Trend tests were run for Cu at one station (Dunkard Creek). Trend 

tests for Fe were run at 12 stations in both time frames, and at the other two stations in one time 

frame or the other. Trend tests for Pb were run at one station (Beaver River) for both time 

frames, and in the 1991 to 2010 time frame at another three stations. Trend tests for Zn were run 

at three stations in both time frames, and at another three stations in the 2000 to 2010 time frame. 

The low number of trends run for Cu and Pb indicate a high proportion of samples reported as 

below detection limits. Statistically significant trends were more commonly seen for the 

transition metals and poor metals in the 1991 to 2010 datasets compared to the 2000 to 2010 

datasets, especially for Al, Pb, and Zn. The three datasets that showed statistically significant 

transition metal and poor metal trends for the 2000 to 2010 period (Al in Kettle Creek, and Cu 

and Fe in Dunkard Creek) also showed statistically significant trends from the 1991 to 2010 

period. Most of the statistically significant transition metal and poor metal trends indicated 

decreases between 30% and 66% over the time periods tested, with trends for Pb – while 

relatively rare – being more dramatic, ranging from 85% to 94%.

Trends for ALK, Hard, and the two alkali earth metals tested (Ca, Mg) were variable (Table 2, 

Table 3). Trends for ALK and Hard were run in both time periods at all 14 stations. Trends for 

Ca and Mg were run at three stations in both time frames, and at the 11 other stations in the 2000 

to 2010 time frame. Statistically significant trends were more commonly observed for ALK and 

Hard in the 1991 to 2010 time frame, and all indicated increasing trends in these two 

constituents. Statistically significant trends for ALK and Hard were less commonly observed in 

the 2000 to 2010 dataset. Five stations showed statistically significant increasing trends in ALK 

from 2000 to 2010 with one station (Clarion River) showing a decreasing ALK trend during this 

time frame. One station (Dunkard Creek) showed a statistically significant increasing Hard trend 

in the 2000 to 2010 time frame, with three stations showing a statistically significant decreasing 

Hard trend during this period. Kettle Creek showed a statistically significant trend for Ca or Mg 

in the 1991 to 2010 time frame – this trend was decreasing for Mg. In the 2000 to 2010 time 

frame, one station (Dunkard Creek) showed increasing trends for both Ca and Mg, while one 

other station (Beaver Falls) showed decreasing trends for both Ca and Mg. Another station 

(Connoquenessing Creek) showed a statistically significant decreasing trend for Ca in the 2000 

to 2010 time frame, and three other stations showed statistically significant decreasing trends for 

Mg in the 2000 to 2010 time frame. Most statistically significant ALK and Hard trends indicated 

increases or decreases between 10% and 50% over the time periods tested, with decreasing 

trends ranging between 9% and 27%. The Youghiogheny River and Dunkard Creek ALK trends 

were more pronounced, and the Dunkard Creek Hard trend was large relative to other Hard 

trends. The statistically significant Ca and Mg decreasing trends were fairly moderate with 

decreases between 7% and 30%, while the statistically significant Dunkard Creek Ca and Mg 

increasing trends indicated increases of 174% and 363%, respectively.

Trends for SO4 and TDS were mostly decreasing, but variable across stations (Table 2, Table 3). 

Trends for SO4 were run at all but one station in both time frames, with SO4 trends at the Oil 

Creek station run in the 2000 to 2010 window. Trends for TDS were run at seven stations in 

both time frames, with trends run at another six stations in the 2000 to 2010 window. There was 

one station (Sinnemahoning Creek) where TDS trends were not run for either time frame. 
55

Statistically significant increasing trends for both SO4 and TDS were observed at one station 

(Dunkard Creek) in both time frames. At another station (Clarion River), statistically significant 

increasing trends were observed for both SO4 and TDS in the 2000 to 2010 time frame with a 

statistically significant increasing trend in SO4 also observed in the 1991 to 2000 time frame. 

Statistically significant decreasing trends for SO4 were observed at 11 stations in the 1991 to 

2010 time frame and at eight stations in the 2000 to 2010 time frame. In the 1991 to 2010 time 

frame, no station showed a statistically significant decreasing TDS trend, but five stations did in 

the 2000 to 2010 time frame. The statistically significant decreasing SO4 and TDS trends mostly 

ranged between decreases of 12% to 35% with a few exceptions of more dramatic decreasing 

SO4 trends. The increasing SO4 and TDS trends at the Dunkard creek station were much more 

pronounced.

Trends for tested nitrogen species (NO3, NH4, TN) were mostly decreasing, but variable across 

stations (Table 2, Table 3). Trends for NO3 were run at all 14 stations in both time frames. 

Trends for NH4 were run at five stations in both time frames. Trends for TN were run at all 14 

stations in the 2000 to 2010 time frame. Two stations (Dunkard Creek, Clarion River) showed 

statistically significant increasing trends in NO3 in both time frames. Both of these stations also 

showed statistically significant increasing trends in TN in the 2000 to 2010 time frame, with the 

Dunkard Creek station also showing statistically significant increasing trends in NH4 in both 

time frames. All other statistically significant trends for nitrogen species indicated decreasing 

trends. Eight stations showed statistically significant decreasing NO3 trends in the 1991 to 2010 

window, while five stations showed statistically significant decreasing NO3 trends in the 2000 to 

2010 window. Two stations showed statistically significant decreasing NH4 trends in the 1991 

to 2010 window, with one station showing a statistically significant decreasing NH4 trend in the 

2000 to 2010 window. Four stations showed statistically significant decreasing TN trends in the 

2000 to 2010 window. The statistically significant decreasing nitrogen species trends mostly 

range between decreases of 22% and 60% with a few exceptions of more dramatic decreasing 

trends. The increasing nitrogen species trends at the Dunkard Creek and Clarion River stations 

were larger than decreasing trends, especially in the 2000 to 2010 window.

Trends for tested phosphorus species (DIP, TP) indicated decreasing trends, except at the 

Dunkard Creek station (Table 2, Table 3). Trends for DIP were run at 11 stations in the 2000 to 

2010 period, with no DIP trend tests run in the 1991 to 2000 window. Trends for TP were run at 

11 stations in both time frames, with TP trends run in the 1991 to 2010 window at two stations, 

and in the 2000 to 2010 window at one station. For DIP, the statistically significant trends 

indicated decreasing trends at five stations in the 2000 to 2010 window. For TP, 10 stations had 

statistically significant decreasing trends in the 1991 to 2010 window. The one statistically 

significant trend for TP in the 2000 to 2010 window was an increasing trend at the Dunkard 

Creek station. The statistically significant decreasing phosphorus species trends tended to be 

larger than decreasing trends for other constituents with most decreasing phosphorus species 

trends ranging between 50% and 82%. The increasing TP trend at Dunkard Creek in the 2000 to 

2010 was estimated to be increasing at 264%.

Trends for TSS were run at all but one station (Kettle Creek) in both time frames (Table 2, Table 

3). The two statistically significant TSS trends were increasing trends at the Clarion River 

station in the 2000 to 2010 period (247%) and at the Oil Creek station in the 1991 to 2010 period 

(138%). Surprisingly, the 2000 to 2010 TSS trend at the Oil Creek station was associated with a 

decreasing TP trend.
56

Table 2. Approximate percent change in flow-adjusted trends over the tested time periods. Highlighted values indicate statistically significant trends (pvalues < 0.05) with yellow indicating increasing trends and orange indicating decreasing trends. --- indicates datasets without enough data to run the trend 

test, where residuals were not normal, or with > 50% non-detects.

WQN Stream Name Start

Year

Al

Cu

Fe

Pb

Zn

ALK

Hard

Ca

Mg

SO4

TDS

NO3NH4

TN

DIP

TP

TSS

WQN

185

Delaware River

at Callicoon, NY

1991 -41 --- --- --- --- 22 30 5 5 -35 --- -17 --- --- --- -63 145

2000 28 --- 44 --- --- 3 0 1 -1 -19 27 5 --- 33 --- -7 156

WQN

317

Tunkhannock Creek

at Tunkhannock, PA

1991 --- --- -30 --- --- 15 25 --- --- -61 --- -39 --- --- --- -54 103

2000 --- --- --- --- --- 5 -1 -1 -7 -8 1 -45 --- -33 -22 -28 144

WQN

402

West Branch 

Susquehanna

River at Williamsport, PA

1991 -52 --- -22 --- -66 46 -2 --- --- -20 -3 -28 -56 --- --- -82 -21

2000 --- --- -4 --- -50 47 -9 -7 -13 -21 -16 -23 -4 -39 -22 -1 1

WQN

418

Sinnemahoning Creek

at Sinnemahoning, PA

1991 --- --- -3 --- --- 29 2 --- --- -22 --- -57 --- --- --- -71 136

2000 --- --- -16 --- --- 3 -9 -6 -12 -13 --- -25 --- -1 --- --- 120

WQN

434

Kettle Creek

near Westport, PA

1991 -37 --- -1 --- --- 6 11 -5 -11 -23 --- -46 --- --- --- -64 ---

2000 -47 --- -19 --- --- -6 -6 -5 -7 -12 4 2 --- -28 -12 --- ---

WQN

706

Youghiogheny River

at Suterville, PA

1991 -62 --- -38 --- --- 53 23 --- --- -18 16 -22 -28 --- --- --- -15

2000 --- --- -33 --- -61 25 -1 -1 0 -4 -12 -29 44 -26 -26 20 18

WQN

714

Dunkard Creek

at Shannopin, PA

1991 -34 -49 -41 --- -46 59 88 --- --- 171 134 152 285 --- --- -19 66

2000 -33 -61 -43 --- -25 15 189 174 363 652 443 244 1258 226 -57 264 97

WQN

805

Allegheny River

at West Hickory, PA

1991 -57 --- -19 --- --- 12 19 --- --- -63 --- -35 --- --- --- -34 20

2000 --- --- -10 --- --- 8 -2 1 -10 -21 7 -32 --- -3 -54 -3 -42

WQN

820

Redbank Creek

at St. Charles, PA

1991 -58 --- -27 -92 --- 40 4 -12 17 -12 11 -14 --- --- --- -64 -2

2000 --- --- 4 --- --- 18 -3 -2 -6 -5 -8 -18 --- -15 --- 46 146

WQN

822

Clarion River

at Cooksburg, PA

1991 --- --- -13 --- --- 10 35 --- --- 67 --- 39 --- --- --- -52 20

2000 --- --- -12 --- 0 -17 -2 2 -9 32 24 258 --- 222 -34 -6 247

WQN

868

Oil Creek

at Rouserville, PA

1991 --- --- 4 --- --- 26 28 --- --- --- --- -17 --- --- --- -47 138

2000 --- --- -22 --- --- 16 -3 -2 -4 -15 -19 -32 --- -31 -9 15 41

WQN

905

Beaver River

at Beaver Falls, PA

1991 -38 --- 24 -85 -63 12 10 --- --- -33 -1 -47 -6 --- --- -19 48

2000 -20 --- -1 -39 -49 3 -11 -14 -13 -22 -23 -38 -53 -24 -55 -9 56

WQN

907

Connoquenessing Creek

near Zelienople, PA

1991 -37 --- -9 -94 --- 22 -10 --- --- -28 -15 -93 -69 --- --- -31 -11

2000 4 --- 34 --- -10 11 -27 -30 -10 -18 -36 -78 -21 -27 -3 50 160

WQN

922

Slippery Rock Creek

at Wurtemburg, PA

1991 -49 --- 23 -84 --- 19 3 --- --- -23 -5 -10 --- --- --- -5 -5

2000 -15 --- 7 --- --- 18 -3 -2 -4 -12 -17 -14 --- -14 -59 8 -37
57

Table 3. Summary of the number of stations with executed trend tests and 

statistically significant trends by time period.

Constituent Start

Year

# of stations

with executed

trend tests

# of stations with 

statistically significant trend tests

increasing decreasing

Al 1991 10 0 9

2000 6 0 1

Cu 1991 1 0 1

2000 1 0 1

Fe 1991 13 0 3

2000 13 0 1

Pb 1991 4 0 4

2000 1 0 0

Zn 1991 3 0 3

2000 6 0 0

ALK 1991 14 13 0

2000 14 5 1

Hard 1991 14 9 0

2000 14 1 3

Ca 1991 3 0 0

2000 14 1 2

Mg 1991 3 0 1

2000 14 1 4

SO4 1991 13 2 11

2000 14 2 8

TDS 1991 7 2 0

2000 13 2 5

NO3 1991 14 2 8

2000 14 2 5

NH4 1991 5 1 2

2000 5 1 1

TN 1991 0 0 0

2000 14 2 4

DIP 1991 0 0 0

2000 11 0 5

TP 1991 13 0 10

2000 12 1 0

TSS 1991 13 1 0

2000 13 1 0

Discussion

The decreasing trends in transition metals, poor metals, SO4, TDS, nitrogen species, and 

phosphorus species, combined with increasing trends in ALK and Hard suggest improving 

chemical water quality conditions based on the sampling conducted in the tested time periods at 

all the stations analyzed except the Dunkard Creek station and Clarion River station. Increasing 
58

trends in ALK can often be considered water quality improvements because increased ALK 

means increased acid neutralizing capacity, but elevation of alkalinity much beyond natural 

levels can have detrimental consequences to water quality, so assessment of the ALK trends 

depends on the specific context of conditions at each station.

Trends for many constituents exhibited particularly dramatic increasing trends at the Dunkard 

Creek station. Increasing trends at this station were well over 100% for Hard, Ca, Mg, SO4, 

TDS, NO3, NH4, TN, and TP in one or both time frames. The Dunkard Creek station and the 

Clarion River station were the only two stations to show increasing SO4 , NO3, and TN trends. 

These two stations, along with the Youghiogheny River station in the 1991 to 2010 time frame –

were also the only stations to show increasing TDS trends, with the increasing TDS trends at 

Dunkard Creek being particularly dramatic. The Dunkard Creek station was also the only station 

to show increasing Ca, Mg, NH4, and TP trends.
59

Part D Groundwater

Part D1. Groundwater Assessment

Ambient/Fixed Station Ground Water Quality Monitoring Network (GWMN):

Resources available to operate the Ambient Fixed Ground Water Monitoring Program continue 

to be limited. Ground water quality monitoring has been active from 2009 to 2011 in three 

GWMN basins: Kirkwood Basin (196), Pottstown Basin (58), and Telford Basin (61) (Figure D1). A total maximum daily load is under development for the Upper Octoraro Creek (Kirkwood 

Basin). The Ground water quality monitoring data for the Kirkwood Basin has been made 

available for this effort. 

Figure D-1

Statewide Monitoring Networks:

To address the need for increased groundwater quality monitoring coverage of the state to meet 

program goals, DEP has worked with the USGS to design a statewide, watershed-based 

groundwater quality network using the stratified approach applied in the USGS National Water 

Quality Assessment project for the lower Susquehanna River. There have been 13 major aquifer 

categories identified for the network based on dominant rock type or geolithologies. The 

distribution of these geolithic units (except for the glacial outwash) are shown on Figure D-2.
60

Figure D-2

To develop the groundwater network, 30 groundwater monitoring points are needed within each 

geolithic unit. This network can be reconfigured to be analyzed based upon various delineated 

watershed. 

Part D2. USGS Groundwater Quality Data Compilation for Pennsylvania

Under a joint funding agreement with the Bureau of Safe Drinking Water, the U.S. Geological 

Survey has updated a digital Data Series report that provides a compilation of electronically 

available groundwater quality data for a 28-year period based on water samples from wells 

throughout Pennsylvania (Figure D-3). Twelve data sources from local, state, and federal 

agencies were used in the updated compilation, which covers 11 different analyte groups. The 

data are presented both in terms of 35 former water planning watersheds used by DEP as well 

as the 13 major geolithologic units representing the major aquifers in the state. Over 24,000 

wells were included in the project and the number of analyses ranged from several thousand for 

nutrients and other inorganic compounds to two dozen for antibiotics. The number of wells 

sampled varies considerably across the state with most being concentrated near major urban 

centers. Minimal data exists for about a fourth of the state. When compared to maximum 

contaminant levels (MCL), the analyte group with the highest MCL exceedance was 

microorganisms (50% of 4,674 samples), followed by volatile organic compounds (24% of 4,528 

samples). The lowest MCL exceedances were for insecticides (<1% of 1,424 samples) and 

wastewater compounds (<1% of 328 samples). With limited monitoring of ambient groundwater 

in only a handful of basins in the Ambient/Fixed Station Monitoring Networks, this compilation 

will help fill in data gaps and shed light on how to establish a more complete statewide 

groundwater monitoring network. This data compilation in addition to capturing compliance 

ground water quality data will help address ground water data needs in the area of 

unconventional hydrocarbon development in the state. The report (Low, D.J., Chichester, D.C. 
61

and Zarr, L.F. 2008. Selected groundwater quality data in Pennsylvania – 1979-2006: USGS 

Data Series 314, 22 p.) is available on-line at http://pubs.usgs.gov/ds/314/ 

Figure D-3

Part D3. Sources of Groundwater Contamination

Each DEP regional office defined its highest priority sources of groundwater contamination. 

These concerns are consistent from the 2008 report and are shown below in Table D-1. The 

priorities include industrial facilities, underground storage tanks, hazardous waste sites, 

abandoned landfills, aboveground storage tanks, manure/fertilizer applications, chemical 

facilities, and septic systems. The contaminants associated with these sources are also shown. 

Multiple regional studies have indicated 30% to 90% of private water wells have total coliform 

contamination. In addition, one study showed up to 30% E. coli contamination. The USGS study 

Relation Between Selected Well Construction Characteristics And Occurrence Of Bacteria In 

Private Household Supply Wells, South-Central And Southeastern Pennsylvania, WRIR 01-

4206, stated that either or both well construction and aquifer contamination could be responsible 

for the results but problems were more likely to occur where the well was poorly constructed.
62

Table D-1. Major Sources of Groundwater Contamination

Contaminant Source

Highest-Priority

Sources (√)

Factors Considered in 

Selecting Contaminant 

Sources (1) Contaminants

Agricultural Activities (2)

Animal feedlots

Chemical facilities √ ADCEFG ABCDE

Drainage wells

Manure/fertilizer applications √ ABCDEFGH DEIK

On site pesticide

mixing/loading

Pesticide applications

Storage/Treatment

Activities

Land application of biosolids

Lawn maintenance/pest

treatment

Material stockpiles

Storage tanks (above ground) √ ABCDEFG ABC

Storage tanks (underground) √ ABCDEFGH ABCDEGIJK

Surface impoundments

Waste piles or tailings

Disposal Activities

Abandoned landfills √ ABCDE ADGJ 

Landfills (current)

Septic systems √ ABCDEFGH EIK 

Underground injections 

wellsResource Extraction

Abandoned/existing oil/gas 

wells Abandoned/poorly built water 

wells Coal mining/acid mine drainage

Quarries (noncoal)/borrow pits

Other

Atmospheric deposition

Industrial facilities √ ABCDEFG ABCG 

Hazardous waste 

generators Hazardous waste sites √ ABCDEFG ABCDEGHIJK

Natural groundwater

conditions (3)

Petroleum/fuel pipelines

Sewer lines

Salt storage and road deicing 

Spill Urban runoff s/transportation of materials
63

(1) Factors in Selecting a Contaminant Source (2) Contaminants

A. Human health and/or environmental risk (toxicity) A. Volatile organic chemicals

B. Size of the population at risk B. Petroleum compounds

C. Location of the source relative to drinking water sources C. MTBE/TBA

D. Number and/or size of contaminant sources D. Pesticides

E. Hydrogeologic sensitivity E. Nitrates

F. State findings, other findings F. Salinity/brine

G. Documented from mandatory reporting G Metals

H. Geographic distribution/occurrence H. Radionuclides

I. Other criteria (please describe) I. Microbiological

J. Sulfates, manganese and/or iron

K. Total dissolved solids

L. Other contaminant (please describe)

(3)This could include natural occurring contaminants such as radium, radon, sulfate, iron, manganese, salt, etc.

Part D4. Statewide Groundwater Protection Programs

A summary of state groundwater protection programs is presented in Table D-2. Important 

groundwater protection programs are summarized following the table. Pennsylvania does not 

have statewide, private water well construction standards.

Table D-2. Summary of State Groundwater Protection Programs

Programs or Activities

Implementation

Status

Responsible

State Agency

Active SARA Title III Program Fully established BLRWM

Ambient groundwater monitoring system Continuing efforts BSDW

Aquifer vulnerability assessment (pesticides) Continuing efforts PDA

Aquifer mapping Continuing efforts BTGS

Aquifer characterization Continuing efforts BTGS

Comprehensive data management system Under development BSDW*

EPA-endorsed Core Comprehensive State

Groundwater Protection Program (CSGWPP)

Partially established BSDW*

Groundwater discharge permits Continuing efforts RWM

Groundwater Best Management Practices Continuing efforts BSDW*

Groundwater legislation (remediation) Fully established BLRWM

Groundwater classification (remediation) Continuing efforts BLRWM

Groundwater quality standards (remediation) Fully established BLRWM

Interagency coordination for groundwater protection 

initiatives

Continuing efforts BSDW*
64

Programs or Activities

Implementation

Status

Responsible

State Agency

Non-point source controls Continuing efforts BPNP*

Pesticide State Management Plan Continuing efforts PDA

Pollution Prevention Plan Continuing efforts OPPCA

Resource Conservation and Recovery Act

(RCRA) Primacy

Fully established BLRWM

Source Water Assessment Program (EPA approved 

2000)

Fully established BSDW

State Superfund Fully established BLRWM

State RCRA Program incorporating more stringent 

requirements than RCRA primacy

Not applicable

State septic system regulations Fully established BPNP

Underground storage tank installation requirements Fully established BLRWM

Underground storage tank remediation fund Fully established BLRWM

Underground storage tank permit program Fully established BLRWM

Underground injection control program Not applicable; EPA direct 

implementation

Vulnerability assessment for drinking water/wellhead 

protection

Partially established BSDW*

Well abandonment guidelines Fully established BTGS*

Wellhead Protection Program (EPA approved 1999) Continuing effort BSDW

Well installation regulations (Public Water Supplies) Fully established BSDW

Others:

Monitoring well installation guidance Fully established BSDW*

Nutrient management program Continuing efforts BCR

Private well installation guidance Continuing efforts BSDW

Voluntary site remediation program Fully established BLRWM

BLRWM DEP Bureau of Environmental Cleanup and Brownfields

BTGS Bureau of Topographic and Geologic Survey, Department of Conservation and

Natural Resources

BCR DEP Bureau of Conservation and Restoration

BPNPM DEP Bureau of Point and Nonpoint Source Management

BSDW DEP Bureau of Safe Drinking Water

OPPCA DEP Office of Pollution Prevention and Energy Assistance 

PDA Bureau of Plant Industry, Department of Agriculture

RWM DEP Regional Water Management Program

* Indicates lead agency

Part D5. Groundwater Protection Program

DEP’s Principles for Groundwater Pollution Prevention and Remediation (DEP ID: 383-0800-

001), is available on DEP's website at 

http://www.portal.state.pa.us/portal/server.pt/community/dep_home/5968
65

and has been in place since 1996. This document sets forth the principles for a consistent 

statewide program for prevention of groundwater pollution and remediation of contaminated 

groundwater. The ultimate goal for groundwater protection, as set forth in the Principles, is 

prevention of groundwater contamination whenever possible.

Part D6. Wellhead Protection and Source Water Protection Program

Pennsylvania’s Wellhead Protection Program (WHP) is the cornerstone of the Source Water 

Assessment and Protection (SWAP) Program for groundwater resources serving public water 

systems. Pennsylvania’s Wellhead Protection Program (WHP) was developed in 1989 and 

subsequently approved by EPA in 1999. The Pennsylvania safe drinking water regulations direct 

public water suppliers to find and utilize the best sources available and take measures necessary 

to protect those sources. These regulations define wellhead protection, set permitting 

requirements for groundwater resources, and set forth requirements for state approval of local 

WHP programs.

More than 600 municipalities or water suppliers are developing or implementing local WHP 

programs and/or watershed protection programs. DEP provides direct technical assistance, and 

supports partnerships to assist communities and water systems to protect community drinking 

water sources from contamination. These efforts and previous grants support the voluntary 

development of local Source Water Protection (SWP) programs that meet DEP's minimum 

requirements. Since 2007, direct technical assistance has been provided to community water 

systems and municipalities through the Source Water Protection Technical Assistance Program. 

Over 90 Community Water Systems (CWS) are participating in the program at this time. In 

addition to protecting public health and infrastructure investment by avoiding costly 

contamination, local SWP efforts complement watershed protection and management through 

sound land-use planning and pollution prevention activities. Source water protection is an 

integral part of a sustainable infrastructure for public water supply.

Part D7. Source Water Assessment and Protection (SWAP) Program

The 1996 Safe Drinking Water Act reauthorization requires that states develop a Source Water 

Assessment and Protection (SWAP) Program. The SWAP program assesses the drinking water 

sources that serve public water systems for their susceptibility to pollution. This information is 

used as a basis for building voluntary, community-based barriers to drinking water 

contamination. States are required to assess all sources (both groundwater and surface water) 

serving public water systems. In Pennsylvania, this represents about 14,000 permanent drinking 

water sources. EPA approved Pennsylvania’s SWAP program in March 2000. Pennsylvania has 

completed the source water assessments for 98% of systems in the state. Under the plan, 

Pennsylvania will continue to conduct assessments for new sources and update completed 

assessments as needed.

For the assessments that have been completed, the SWAP program has delineated the boundaries 

of the areas providing source waters for all public water systems and has identified (to the extent 

practicable) the origins of regulated and certain unregulated contaminants in the delineated area 

to determine the susceptibility of the water sources to such contaminants. 
66

The SWAP program provides prioritized information on the potential sources of contamination 

that will be the basis for coordination of restoration efforts and development of local source 

water protection programs. These efforts will lead to improvements in raw water quality and 

may also result in reduced treatment costs for the public water system. The following table 

provides a summary of the results of the source water assessments for the most common and the 

most threatening potential sources of contamination to sources of public drinking water 

conducted under the EPA Program. More detail on how the source water assessments 

were conducted can be found in the Source Water Assessment and Protection Program 

guidance.

Table D-3. Most Prevalent and Threatening Sources of Contamination

GW 

RANK 

EPA Most Threatening EPA Most Prevalent

1 Underground Storage Tanks Transportation Corridors

2 Transportation Corridors Agriculture

3 Agriculture Underground Storage Tanks

4 Automobile Related Activities Septic

5 Mining Mining

SW 

RANK 

EPA Most Threatening EPA Most Prevalent

1 Transportation Corridors Transportation Corridors

2 Agriculture Municipal Sanitary Waste Disposal

3 Fertilizer and Pesticide Applications Septic Systems

4 Storm water Mining

5 Mining Animal Feeding Operations

GW 

RANK 

EPA Most Threatening EPA Most Prevalent

1 Underground Storage Tanks Transportation Corridors

2 Transportation Corridors Agriculture

3 Agriculture Underground Storage Tanks

4 Automobile Related Activities Septic

5 Mining Mining

SW 

RANK 

EPA Most Threatening EPA Most Prevalent

1 Transportation Corridors Transportation Corridors

2 Agriculture Municipal Sanitary Waste Disposal

3 Fertilizer and Pesticide Applications Septic Systems

4 Storm water Mining

5 Mining Animal Feeding Operations

GW 

RANK 

EPA Most Threatening EPA Most Prevalent

1 Underground Storage Tanks Transportation Corridors

2 Transportation Corridors Agriculture

3 Agriculture Underground Storage Tanks

4 Automobile Related Activities Septic

5 Mining Mining

SW 

RANK 

EPA Most Threatening EPA Most Prevalent

1 Transportation Corridors Transportation Corridors

2 Agriculture Municipal Sanitary Waste Disposal

3 Fertilizer and Pesticide Applications Septic Systems

4 Storm water Mining

5 Mining Animal Feeding Operations

Source water assessments support emergency response, improved land use planning and 

municipal decisions. They also prioritize and help coordinate actions by federal and state 

agencies to better protect public health and safety. Spill detection and emergency response 

networks for public water systems in Pennsylvania have been established on the Allegheny, 

Monongahela, Susquehanna, Schuylkill, and Delaware Rivers. They include a variety of on-line 

detectors to alert operators to imminent changes in raw water quality at surface water intakes. 

Long-term trends in raw water conditions based on data provided by these monitors may be the 

basis for restoration and protection efforts or changes in water treatment schedules. The core of 

these programs is the Internet based communication network that shares raw water data, incident 

information, and response efforts in real-time.