New York State has established and implemented various programs and initiatives to research water quality issues throughout the state relating to Harmful Algal Blooms.

In 2017 New York State established the Finger Lakes Watershed Hub, a core team of NYSDEC scientists who work collaboratively with stakeholders throughout the Finger Lakes region to better understand, protect and address the water quality issues confronting the lakes, which are part of the Great Lakes watershed in New York.

In 2018, New York State Governor Cuomo announced a $65 million, four-point initiative to aggressively combat HABs in twelve priority lakes that have experienced or are vulnerable to HABs, including five of the Finger Lakes that are in the Lake Ontario watershed: Conesus, Honeoye, Cayuga, Owasco, and Skaneateles Lakes. The components of the initiative include: convening four regional summits bringing together agency representatives, stakeholders, and national water quality/HAB experts; developing Action Plans and providing nearly $60 million in grant funding for implementation; in-lake mitigation pilot projects; and, conducting advanced research and monitoring.  The Action Plans for the Finger Lakes were released in June 2018 and include priority actions that range from wastewater treatment upgrades, sewer expansions, and septic system upgrades and replacements, to streambank erosion prevention, stormwater best management practices, agricultural nutrient reduction measures, and open space buffer preservation projects.  For the remaining Finger Lakes not included in the HAB initiative, other types of Clean Water Plans (TMDL or watershed plan) are being developed. While these efforts are not directly applicable to Lake Erie, they will inform any future efforts that may be needed to address related water quality issues that may appear in the Lake Erie watershed.