There are many different state agencies involved in water quality management. This short guide provides a bit of detail on each of the different agencies, people to contact for specific questions, as well as an outline of the responsibilities of each agency.
Shellfish Communities
There are over 60 coastal communities with shellfish ordinances in Maine. Generally, this requires the creation of the marine resource or shellfish committee, and a shellfish ordinance that discusses species harvested, specific localized restrictions, and licensing information. Shellfish communities are generally responsible for a lot of the leg work in terms of resolving water quality issues. This is done through extensive scientific projects, either increased water testing, surveying shorelines for any specific pollution problems or other methods.
State Agencies
The Department of Marine Resources (DMR)

The DMR is an organization established to conserve and develop marine and estuarine resources and advise and cooperate with local, state, and federal officials concerning activities in coastal waters. The DMR oversees water quality testing and regulation, and makes decisions around water quality closures. The DMR also advises the Shellfish Advisory Council on different legislative proposals to State management. To reach more about the Department of Marine Resources, please visit their website, here.
The Department of Environmental Protection (DEP)

The DEP is an organization focused on environmental protection. In shellfish management, DEP focuses on enforcement around rivers and sewage systems. Members of the DEP have often collaborated with towns to facilitate waste discharge restoration projects as well as others. To read more about the DEP, please visit their website, here.
The Department of Health and Human Services (DHHS)

The Department of Health and Human Services (DHHS) through the Maine Subsurface Wastewater Team, works to test and determine if subsurface sewage systems are depositing fecal coliform bacteria into nearby soils, estuaries, or rivers. To read more, please visit their website, here.
The Department of Inland Fisheries and Wildlife

The Department of Inland Fisheries and Wildlife (MDIFW) does not have any direct management over the soft-shell clam fishery or other coastal fisheries. However, they should be consulted if wildlife is determined to be the source of water quality issues, in order to find if remediation is possible. For example, if a town were to find a flock of geese or beaver dam were creating a water quality issue, the MDIFW should be consulted to understand how to approach that problem. For more information, please visit their website, here.
The Department of Agriculture, Conservation and Forestry

The Department of Agriculture, Conservation and Forestry (DACF) does not directly manage the soft-shell clam fishery, but can help communities who believe water quality issues can be attributed to agriculture. This is rarely the case, however, this agency works well in devising plans with community members and farmers to create workable solutions. For more information, please visit their website, here.