The impacts of historical industry within the region are still felt today, with legacy pollution from tanneries, paper mills, and chemical companies impacting water quality and sediment in the rivers and bay, including mercury contamination from HoltraChem that impacted the Penobscot River and Penobscot Bay. Historical use of contaminated sludge on farmland is an emerging issue in Maine.  Beginning in 2021, Maine began testing more than 1,000 farms due to ​​the spreading of PFAS contaminated sludge on agricultural fields. Results showed 50+ farms with soils and groundwater with extremely high levels of PFAS. Maine has also begun testing 1,600+ drinking water wells for PFAS contamination. While 75% of those passed, the state standard for PFAS in drinking water is 20 parts per trillion and standing testing only includes 6 different types of PFAS.

Like state resource agencies across the country, Maine’s Department of Environmental Protection, the agency responsible for protecting and restoring Maine's natural resources and enforcing the state's environmental laws, is understaffed and underfunded. Based on a 2019 report from the Environmental Working Group entitled “Thin Green Line” that evaluated cuts in state pollution control agencies between 2008 and 2018, Maine agency budgets decreased 17%, and there was a 10% reduction in agency staff. Through our efforts against Nordic Aquafarms, we have seen the governor’s administration and state enforcement agencies line up behind a project at the expense of the environment, and true public input processes. Upstream Watch’s work opposing Nordic has highlighted the need for oversight of environmental regulatory agencies, their permitting decisions, and their enforcement actions.

Large-scale, industrial aquaculture is a growing issue in the Penobscot Bay region, and throughout Maine generally. There have been a number of recent industrial aquaculture proposals other than Nordic’s Belfast proposal, including in Bucksport at the mouth of the Penobscot River, and Millinocket, further upstream in the watershed. The Governor’s administration has publicly supported the aquaculture industry and its expansion into Maine despite the potential negative impacts not only to the environment and the state’s climate commitments, but also to the fishing and tourism economies of the coast.

The Gulf of Maine, of which Penobscot Bay is an inlet, is one of the fastest warming bodies of water on the planet. Over the last 30 years, the Gulf of Maine warmed at a rate of 0.11°F per year - more than three times the global average. The Gulf is beginning to lose its subarctic characteristics, and recently has experienced “marine heat waves,” which occur when an area of the ocean experiences temperatures above the 90th percentile for more than five consecutive days. Ocean warming, acidification, and sea level rise are already affecting ecosystems and coastal areas, and will continue to accelerate as the climate warms.

Atlantic salmon in the United States were once native to almost every coastal river northeast of the Hudson River in New York. But dams, pollution, and overfishing reduced their population size until the fishery was closed in 1948. The Penobscot River watershed is one of only a few other waterways in Maine that support the last remaining wild Atlantic salmon in the United States.

Due to aging stormwater and sewage infrastructure, as well as increased development and growing year round populations in formerly seasonal communities, sewage and stormwater are issues in the basin, specifically in the growing coastal communities and Route 1 corridor. There are at least 17 Wastewater Treatment Plants along the Penobscot, with eight municipalities, including the largest city in the region (Bangor) that still have combined sewer systems and result in combined sewer overflows. Additionally, aging and failing septic systems are a problem in coastal communities along the Bay.