The aquaculture sector has experienced fast growth as a result of livelihood diversification initiatives among small-scale farmers in Tanzania. Regrettably, the dynamics of harmful algal blooms (HABs) have been overlooked despite the noticeable forcing of climate variability, the interaction between social-economic activities, and domestic water supply reservoirs. This study aimed at surveying the occurrence, experiences, and perceptions of HABs in aquaculture systems from stakeholders in the Ngerengere catchment, Morogoro, Tanzania. A cross-sectional survey focus group discussion (FDG), key informant interviews, and anecdotal observation were adopted. A convenient and purposive sample population was drawn from pond owners, registered water users, and government officials in the catchment. For data analysis, descriptive statistics and constant comparison were performed. Most respondents (95%) were able to recognize the image of blooms displayed. Approximately 70% of the respondents agreed that water quality has deteriorated over time, and blooms occur during the dry season. Further, 60% of the respondents agreed that water pollution is a serious problem attributed to sources other than industrial discharge. There was no consensus regarding the health impacts associated with HABs. Raising awareness on HABs is of paramount importance as it will provide the basis for the development of HABs management framework and health risk assessment.