Available guidance to mitigate health risks from exposure to freshwater harmful algal blooms (HABs) is largely derived from temperate ecosystems. Yet in tropical ecosystems, HABs can occur year-round, and resource-dependent populations face multiple routes of exposure to toxic components. Along Winam Gulf, Lake Victoria, Kenya, fisher communities rely on lake water contaminated with microcystins (MCs) from HABs. In these peri-urban communities near Kisumu, we tested hypotheses that MCs exceed exposure guidelines across seasons, and persistent HABs present a chronic risk to fisher communities through ingestion with minimal water treatment and frequent, direct contact. We tested source waters at eleven communities across dry and rainy seasons from September 2015 through May 2016. We measured MCs, other metabolites, physicochemical parameters, chlorophyll a, phytoplankton abundance and diversity, and fecal indicators. We then selected four communities for interviews about water sources, usage, and treatment. Greater than 30% of source water samples exceeded WHO drinking water guidelines for MCs (1μg/L), and over 60% of source water samples exceeded USEPA guidelines for children and immunocompromised individuals. 50% of households reported sole use of raw lake water for drinking and household use, with alternate sources including rain and boreholes. Household chlorination was the most widespread treatment utilized. At this tropical, eutrophic lake, HABs pose a year-round health risk for fisher communities in resource -limited settings. Community-based solutions and site-specific guidance for Kisumu Bay and similarly impacted regions is needed to address a chronic health exposure likely to increase in severity and duration with global climate change.