Harmful algal blooms (HABs) are an increasing threat to water quality and our use of waterbodies. Freshwater HABs are most commonly caused by cyanobacteria, or blue-green algae, that are capable of producing toxins harmful to humans and animals. Benthic (attached) cyanobacteria, the focus of this study, are not well studied or routinely monitored, particularly in lake systems. To address this knowledge gap, we studied benthic cyanobacteria growth and toxin production in nearshore areas of New York lakes where recreational activity, such as boating and swimming, and therefore exposure to cyanotoxins, is potentially high. We applied various field and laboratory methods to characterize benthic cyanobacteria communities and evaluate their potential to produce cyanotoxins.