Water Quality Threats
The New England Interstate Water Pollution Control Commission issued a report in early 1998 on water quality threats that are beyond the abilities of local and state governments to address and resolve on their own. "The Health of the Watershed" identifies specific locations of problems such as toxins in the River (e.g., PCBs), combined sewer overflows (CSOs), bio-accumulation of contaminants, and nonpoint source pollution. CSOs cause temporary Class C conditions in urban areas after storm events. All four of the watershed states have public health advisories on consumption of fish.

Habitat Loss and Fragmentation
A comprehensive inventory and assessment of critical fish and wildlife habitats in the watershed was conducted by the U.S. Fish & Wildlife Service for the Conte Refuge. Habitat loss and fragmentation were found to be significant threats to the rich bio-diversity of the Connecticut River Valley. The Service identified 142,000 acres as "special focus areas" that warrant protection, either because of the presence of protected species or to maintain bio-diversity.

Air Pollution
Acid precipitation and atmospheric deposition of mercury and other contaminants are a problem throughout the watershed. While some sources are local, most sources of air pollution affecting the watershed are outside the region.

Hydroelectric Dams
The Connecticut is one of the most developed rivers in the Northeast, with 16 dams that affect water quality, flow, fisheries, and other river aspects. Federal operating licenses for all of the dams are beginning to come up for renewal. Before each new 40-50 year license is issued, the Federal Energy Regulatory Commission, state agencies, and interest groups like the Watershed Council will examine the proposed operation of each hydroelectric facility to insure it is balanced with protection of the River and its recreational and natural values.

Zebra Mussels and other Invasive Species
A number of invasive species have taken hold in the watershed and threaten native species. These include: common reed (Phragmites), purple loosestrife, Eurasian milfoil and water chestnut; also, mute swans, asiatic clams, and wooly adelgid. Fortunately, the Connecticut has not yet been invaded by Zebra mussels. Their threat is very real, however, as they have taken hold and become a major scourge in nearby waters, e.g., the Hudson River and Lake Champlain.