Long Island Sound Improvement Act Amendments of 2011

Long Island Sound Improvement Act Amendments of 2011 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to create additional duties for the Long Island Sound Office of the Environmental Protection Agency (EPA), including studying the impacts of climate change on the Sound watershed.

Requires a municipality that owns or operates a municipal separate storm sewer system to obtain, without regard to the size of the population served by the system, a permit for discharges composed entirely of stormwater for any portion of the municipality that is located within both the Long Island Sound watershed and an urbanized area. Authorizes such permits to be issued on a regional basis.

Requires the EPA Administrator to ensure that: (1) permits held by industrial stormwater dischargers and permits held by construction activity dischargers conform to regional permits' conditions, and (2) monitoring requirements are included in a regional permit.

Authorizes the Administrator to provide technical assistance to municipalities with respect to establishing regional permits. Establishes: (1) reporting requirements for the Office; and (2) requirements directing agencies to ensure that their property, actions, and activities within the watershed are consistent with the Long Island Sound Comprehensive Conservation and Management Plan (Plan) and to develop plans to maximize forest cover and riparian habitat and minimize stormwater discharge on agency property.

Requires the Administrator to establish a voluntary interstate nitrogen trading program with respect to the Sound that includes the generation, trading, and use of nitrogen credits to facilitate the attainment and maintenance of the Sound Total Maximum Daily Load (TMDL). Authorizes: (1) grants for a prioritized list of projects and studies that will assist in meeting the Plan's goals and objectives; and (2) the Administrator to make grants for the construction of a publicly owned treatment work within Connecticut, Massachusetts, New Hampshire, New York, Rhode Island, and Vermont solely to a municipal or state agency if the state has established allocations for discharges within the state in a Long Island Sound TMDL.

Requires the Administrator to implement a pilot project to demonstrate the efficacy of nutrient bioextraction for the removal of nitrogen and phosphorous from the waters of the Sound watershed.