Large lakes provide a variety of ecological services to surrounding cities and communities. Many of these services are supported by ecological processes that are threatened by the increasing prevalence of cyanobacterial blooms which occur as aquatic ecosystems experience cultural eutrophication. Over the past 10 years, Lake Erie experienced cyanobacterial blooms of increasing severity and frequency, which have resulted in impaired drinking water for the surrounding communities. Cyanobacterial blooms may impact ecological processes that support other services, but many of these impacts have not been documented. Secondary production (production of primary consumers) is an important process that supports economically important higher trophic levels. Cyanobacterial blooms may influence secondary production because 1) cyanobacteria are a poor quality food resource and 2) cyanotoxins may be harmful to consumers. Over three years at 36 sites across the western basin of Lake Erie, we measured 3 indices of secondary production: growth of a native unionid mussel, the size of young-of-year dreissenid mussels, and the mass of colonizing animals on a Hester-Dendy sampler. These indices were related to models with and without cyanobacterial data to assess whether cyanobacteria are associated with variation in secondary production in the western basin of Lake Erie. The results suggest cyanobacterial abundance alone is only weakly associated with secondary production, but that cyanotoxins have a bigger effect on secondary production. Given recent summer’s high cyanobacteria abundance, this impact on secondary production has the potential to undermine Lake Erie’s ability to support important ecosystem services.