Keuka Lake has experienced harmful algal blooms (HABs) in the past but to a much lesser extent than nearby Canandaigua Lake. HABs are a concern because they are capable of producing cyanotoxins which can be. harmful to humans, pets, and wildlife. Nutrient runoff and weather conditions are most often associated with HAB formation. Lakeshore owners around Keuka Lake can help reduce the occurrence of HABs by limiting the use of fertilizers and maintaining healthy lakeshore buffers.

Keuka Lake is home to several invasive species, including Eurasian watermilfoil, Asian clam, and zebra mussels. The best method to prevent the spread of invasive species is to clean, drain, and dry your boat whenever launching or retrieving from a waterbody. If you are fishing Keuka Lake be sure not to dump bait buckets and to clean your gear before and after visiting. Some invasive species are difficult to see with the naked eye and can hide among fishing gear.