- Marine Biotoxin Monitoring - monitors levels of PSP ("Red Tide") and other marine biotoxins in Maine shellfish
- Shellfish Dealer Certification and Inspection - evaluates and certifies Maine wholesale shellfish dealers
- Shellfish Growing Area Classification - monitors the water quality at Maine shellfish flats and conducts shoreline surveys to identify sources of pollution
- Nearshore Marine Resources Program - assists towns in managing their flats and shellfish. Marine Resource Scientists help towns with their conservation areas, reseeding, surveying, town license allocations, shellfish ordinances, warden programs, and more.
- Volunteer Programs - water quality and phytoplankton monitoring
- Environmental Permit Review - conducts/coordinates environmental impact reviews for permits and projects in the coastal zone, involving regulated activities such as wetland alteration, pollution discharge, and dredging/dredge material disposal. The program is also responsible for reviewing projects seeking leases on publicly owned submerged and/or inter-tidal lands, which could have an effect on Maine's fisheries infrastructure, as well as reviewing and commenting on municipal comprehensive plans which may affect marine, estuarine and riverine resources.