Lake Victoria has experienced progressive eutrophication which has exacerbated the proliferation of cyanobacterial harmful algal blooms (cHABs). Fueled by anthropogenic nutrient loadings and climate change, these cHABs are increasing in distribution, duration, and frequency, particularly in areas such as the Winam Gulf. With limited resources and infrastructure, local communities have been left vulnerable as they rely on the lake for water for domestic use. Our study presents the results of a localized survey on how small-scale fishing communities perceive and respond to the threat of cHABs in the Winam Gulf of Lake Victoria, Kenya. We used a mixed-methods approach of quantitative and qualitative data-gathering techniques to elucidate the perceptions and consequences of cHABs in local communities. Our results demonstrate most (93.67%) respondents were aware of cHABs in the lake, but were not knowledgeable of cHAB threats to human and animal health. Respondents noted that fish catches decreased during cHABs, with this economic consequence serving as a primary concern of communities. Notably, respondents altered their use of lake water during perceived cHAB events and relied on other means of water treatment or alternative water sources. Overall, cHAB information was self-sourced or passed on from community elders, with no public mechanism for adequate cHAB risk communication. Lake Victoria serves as a critical resource to the Eastern African region and requires a concerted cHAB response effort. Therefore, we recommend the development of a public awareness program to reduce cHAB exposure in these at-risk communities.