Agricultural Wastewater 

NEW:  Report Water Pollution Concerns here

Use the above link to report concerns related to water pollution. Submitted complaints are reviewed on an ongoing basis and will be investigated in accordance with the potential environmental harm and risk to public safety.

If you are representing a municipality and you are reporting a bypass, use the reporting instructions found on the Bypass Reporting for Municipalities webpage.

If your complaint is an environmental emergency, call DEEP's Emergency Response Unit 24 hours a day at 866-DEP-SPIL (866-337-7745) or 860-424-3338. Please see DEEP's Reporting Environmental Concerns and Problems webpage for additional reporting guidance.

NEW: Online Noncompliance Reporting
Effective December 1, 2023, DEEP’s Water Permitting and Enforcement Division (“WPED”) is receiving noncompliance notifications and follow-up reports required under RCSA Section 22a-430 electronically using a web-based platform. The online noncompliance notification and report forms should be used by facilities with discharge permits issued by WPED to report instances of permit noncompliance including but not limited to effluent limit violations, equipment malfunctions, spills, and bypasses. These forms do not replace DEEP’s 24-hour/day Emergency Response Unit call hotline.

Submit a notification of noncompliance here.
Submit a noncompliance follow-up report here.

How are agriculture and wastewater related?
Agriculture is a dynamic industry in Connecticut, contributing $2 billion to our economy each year. Agricultural activity includes the production of crops and the raising of livestock.

Agricultural wastewater generated from a variety of farm activities, including animal feeding operations and the processing of agricultural products, can pollute surface and ground water if not properly managed. Examples of agricultural wastewater include but are not limited to manure, milking center wash water, barnyard and feedlot runoff, egg washing and processing, slaughterhouse wastewaters, horse washing waters and runoff associated with composting. Additionally, runoff from croplands can contribute sediment, fertilizers and pesticides into surface waters.


EPA Press Release: Office of Agriculture & Rural Affairs

On March 1, 2024, the U.S. Environmental Protection Agency announced that it is establishing a new office to expand engagement opportunities with agricultural and rural communities. The creation of the first-ever EPA Office of Agriculture and Rural Affairs represents the Biden-Harris Administration’s ongoing commitment to improving environmental stewardship and economic opportunity for America’s farmers and ranchers, as well as strengthening the vitality of small towns and rural communities.


“Farmers and ranchers are crucial partners as we work together to deliver clean air, clear water, and climate solutions, all while playing the critical role of ensuring an abundant fiber, fuel and food supply,” said EPA Administrator Michael S. Regan. “With the launch of this new office, we are ensuring agricultural and rural stakeholders will continue to have a seat at the table for many years to come.”

Read more about the new partnership: EPA Press Release.

CT DEEP has also developed an Informational Flyer for Concentrated Animal Feeding Operations.


Concentrated Animal Feeding Operations General Permit (CAFO GP)
Pursuant to EPA’s Concentrated Animal Feeding Operations (CAFOs) Program with the purpose of controlling discharges of agricultural wastewater and stormwater from areas of animal confinement, feeding and maintenance at CAFOs, CT DEEP has issued the General Permit for Concentrated Animal Feeding Operations (CAFO GP) which authorizes new and existing discharges from Large and Medium CAFOs and facilities designated as CAFOs. The CAFO GP is effective January 1, 2023. Links to the general permit, factsheet, response to public comments and the public notice of issuance can be found here:
General Permit for Concentrated Animal Feeding Operations (CAFO GP)
Fact Sheet for the CAFO GP
Response to Public Comments for the CAFO GP
December 12
, 2022 Public Notice of Issuance

The CAFO GP, the CAFO GP registration form, and the registration form instructions can be found on DEEP’s Water Discharge Permits and General Permits webpage.

Facilities that meet the definition of a CAFO, as defined in 40 CFR 122.23(b), but do not meet the requirements of the CAFO GP may need to obtain an individual NPDES permit. Information regarding registration under an individual NPDES permit can be found on DEEP’s Water Discharge Permits and General Permits webpage.

Questions pertaining to discharge permits for CAFOs can be sent to


Partnership for Assistance on Agricultural Waste Management Systems
Connecticut is able to offer technical and financial support to farm businesses in their farm waste efforts through the "Partnership for Assistance on Agricultural Waste Management Systems." This partnership includes the following agencies: USDA Natural Resources Conservation Service (NRCS), USDA Farm Service Agency, University of Connecticut Cooperative Extension System, Connecticut Conservation Districts, the Connecticut Department of Energy and Environmental Protection and the Connecticut Department of Agriculture.

Through this partnership, a farm business may obtain waste management planning, structure design and qualify for financial assistance as well as help in procuring required permits. For further information, contact:

Connecticut Department of Agriculture
Environmental Assistance Program
450 Columbus Boulevard
Hartford, CT 06103
Phone: (860) 713-2511

USDA Farm Service Agency
344 Merrow Road
Tolland, CT 06084
Phone: (860) 871-2944

USDA Natural Resources Conservation Service
344 Merrow Road
Tolland, CT 06084
Phone: (860) 871-4011
Fax: (860) 871-4054

Financial Assistance:

Environmental Quality Incentives Program (EQIP) (link to Natural Resources Conservation Service) 


USDA Natural Resources Conservation Service (NRCS) Technical Resources

Technical Report on Impact of General Permit on Concentrated Animal Feeding Operations in Connecticut (March 2003)

Feasibility Study for Alternative Technologies and Utilization for Managing Dairy and Poultry (December 2005)

Best Management Practices for Agriculture (1996)

Related Info:

Connecticut's Coastal Nonpoint Source Pollution Control Program - Agriculture

Content Last Updated June 5, 2024