TEP Bacterial Monitoring Program

Tillamook Bay and several of its tributaries do not meet state and federal water quality standards for bacteria under the Clean Water Act. In streams and rivers, E. coli bacteria levels often exceed the recreational standard. In the bay, bacteria levels exceed the shellfish harvest standard, causing frequent closures of shellfishing areas. Bacteria contamination is a significant threat to public health and aquatic function, and originates from point and non-point sources in runoff from agricultural, urban, and residential land uses along the rivers. TEP is monitoring bacteria to assess the severity and extent of watershed pollution, identify the most important bacteria sources, and document improvements in response to pollution-abatement measures. To meet these goals, TEP combined volunteer citizen monitoring, routine and storm-based sampling, and innovative DNA tracking methods. This 2008 white paper summarizes TEP's bacteria monitoring program in detail, including information about our bacteria monitoring strategies, our volunteer program background and results, bacteria source tracking, and how we are using monitoring results now and how they will help us target water quality efforts in the future.

To see technical reports on bacteria, click here.
To watch a video about Bacteria Status, Trends, and Source Analysis, click here.

Bacteria Monitoring Strategy

The CCMP's strategy for bacteria monitoring seeks answers to two key questions:

1. Is bacteria loading to the lower reaches of tributary rivers increasing or decreasing over years to decades?


2. Where, how often, and for what length of time do each of the five major tributary rivers violate state water quality standards for bacteria?

To answer these questions, the Partnership initiated complementary monitoring approaches in 1995: the Storm-Based Monitoring Program and the Volunteer Monitoring Program. Then, in 2000, the Partnership embarked on an exciting third approach with Oregon State University: a Bacteria Genetic Marker Study of Tillamook Bay. This 3-year research study will try to identify bacterial pollution sources through DNA fingerprinting of bacteria in water samples and comparing them with DNA from known bacterial sources.

Storm-Based Monitoring

During rain events, which happen often between October and April, the bay is closed to commercial shellfish harvesting due to elevated bacteria levels. The most severe bacteria loading of the lower tributaries usually occurs episodically as a result of stormwater runoff. The Storm-Based Monitoring Program measured fecal coliform bacteria concentrations and loads (and other water quality parameters) during storms. Between 1996 and 2002, 28 separate storms were monitored along four tributaries. The Partnership evaluated trends in bacterial contamination according to season, storm type, precipitation and hydrology before and during storms. With enough data (10+ years), long-term declines in bacteria loading should occur if pollution abatement measures are implemented.

Storm-Based Monitoring showed that there are seasonal differences in fecal coliform levels in all rivers, with fall storm events causing the highest levels, probably due to bacteria buildup during dry periods that "flushes" to rivers during early fall storms. Bacteria concentrations increased dramatically during storms and varied greatly between rivers; some rivers exceeded the recreational standard for most storms sampled, while others sporadically exceeded this threshold. Bacteria concentrations in rivers were strongly influenced by frequency, timing and intensity of rainfall events. Drier conditions before storms and greater rainfall amounts generally resulted in higher bacteria levels. After six years of baseline monitoring, no trends in improvement in water quality were observed.

To identify major bacteria sources, storms were intensively monitored for 2 years along two river reaches that were suspected to be major bacteria-contributing areas. Ten sites were monitored along 2-kilometer sections of the lower Trask River and the lower Wilson River. Potential bacteria sources were documented and mapped using photos, GPS, and field surveys, to attempt to link bacteria concentration spikes to likely sources. Results are being used to identify and prioritize important source areas for corrective actions.

Volunteer Monitoring

Since 1995, volunteers have been braving wind, rain, sleet and sun to collect water samples from the Miami, Kilchis, Trask, Tillamook, and Wilson Rivers. Samples are collected from 37 locations in the watershed, representing many land uses, and are analyzed for E. coli

Microscopic View of E. Coli

bacteria at the Partnership's laboratory. Monitoring results are entered into a long-term database shared with local and state partners. The goal of monitoring is to compare actual water quality to the state's bacteria water quality standard, to document areas of chronic water quality pollution, and to link bacteria pollution to land uses.

The Volunteer Monitoring program showed that all five of Tillamook Bay's main tributary rivers routinely violate Oregon's bacteria water quality standard for water contact recreation. Bacteria concentrations peak during the summer when river flows are low and during some fall, winter and spring storms. The Tillamook River routinely has the highest bacteria concentrations of the five rivers.

View the TEP's Volunteer Monitoring Quality Assurance Protection Plan here.

Genetic Marker Study

Since 2000, citizen volunteers have also been collecting samples for the DNA Marker Study, led by Oregon State University (OSU) researchers. The OSU study seeks to identify bacteria sources by detecting host-specific genetic marker sequences. The goal is to be able to discriminate between fecal bacteria from humans, livestock, domestic pets, waterfowl, and other wildlife, and to measure relative bacterial loading from these sources to the rivers and bay.

So far, the DNA study reliably discriminates between bacteria from humans and bacteria from bovine (cattle) sources. Early results indicate widespread contamination from cows and significant contamination from humans in certain river segments. Bacteria contamination from bovine sources was detected at all sites at least 75% of the time, whereas contamination from human sources was detected much less frequently and at 20-50% of the sampling sites, depending on the river.

Use of Monitoring Results

Any monitoring study should ask "what is the practical relevance of the monitoring results?" Here, the Partnership is using bacteria monitoring results to guide pollution abatement efforts.

Water Quality Monitoring Program Volunteer Pulls an Early Morning Sample from the Tillamook River

The Storm-Based Monitoring Program quantified bacteria loads to the bay from four main tributary rivers. The Tillamook River was documented as the most severely contaminated river. Focusing on corrective actions along this river would result in the most "bang for the buck" in terms of improving water quality. Intensive storm-based monitoring on the lower Wilson and Trask Rivers also revealed "hotspots" that are top priorities for improvement; these include municipal storm water drains, sewage outfalls, and agricultural ditches.

The Volunteer Monitoring Program generated a spatiotemporal picture of bacteria contamination in the watershed. Chronic problems were documented along specific river reaches. This information was crucial for developing a bacteria Total Maximum Daily Load (TMDL) for the watershed, as required by the Clean Water Act, and to prioritize areas for remediation. The Tillamook River had chronically high bacteria concentrations, confirming the Storm-Based Monitoring results.

The Genetic Marker Study helped identify areas of the lower rivers that are contaminated with bacteria from cows, humans, or both. Areas that regularly test positive for human sources of bacteria indicate failing septic systems or sewage treatment plant overflows/failures. Bacterial contamination from cows was widespread throughout the Tillamook lowlands, pointing to the need to continue improving farm management practices. This source-tracking approach provides a powerful scientific tool to guide mitigation and convince the public and policy-makers to address problem sources.

These programs also established an excellent reference database, to use as a yardstick for comparing future water quality. As corrective measures are undertaken, such as improvements in land use practices, sewer treatment plants, private septic systems, and stormwater management, it will be important to document success in cleaning up bacteria sources.

Next Steps

These results have led the Program to undertake several priority projects to reduce bacteria contamination of the bay:

• City of Tillamook and Bay City Stormwater Management Plans - These plans identify stormwater contaminants and measures to reduce bacterial loading, total suspended solids, oils, and inorganic pollutants at outfalls entering rivers. Implementation of these plans is underway.
• Buffer Strip Effectiveness Study - This project tests an experimental demonstration buffer strip to determine its effectiveness in removing bacteria from pasture runoff and to help select BMPs for manure management. The Final Report is available here.
• Performance-Based Environmental Policies for Agriculture - This is a pilot project to develop and implement performance-based policies for agriculture, to meet or exceed water quality standards in the lower basin. In March 2003, TEP was one of six watershed organizations nationwide invited to participate in a workshop hosted by Winrock International and the Farm Foundation. Called "Performance-based Environmental Policies for Agriculture", the workshop facilitated sessions to design market-based approaches to improving agricultural management of water quality. TEP convened a group of six people with backgrounds in agriculture, and the group participated in the workshop in Washington DC. Project managers are pursuing funding for the second phase of the project, which will take place on-site.