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As the number of inhabitants in Sub-Saharan Africa (SSA) increases, demand for animal-source proteins outstrips the current supply. Aquaculture is promoted to sustain livelihood and for improved food security. However, the production in SSA is still low at less than 1% of the total global production. Poor water quality is cited to be one of the factors limiting the growth of the aquaculture sector and is attributed to limited familiarity with standard aquaculture practices. Thus, a knowledge, attitudes, and practices (KAPs) survey was carried out among fish farmers in five districts of the Rwenzori region. Our results showed that 81% and 80% of them had poor knowledge and practices concerning water quality in aquaculture, respectively. Seventy percent did not know that fish farming caused pollution, while 68% believed that there was no need to treat fish farm effluents. Only 45% showed good attitudes towards water quality management. Fish farmers that fed fish with only complete pellets and those that combined them with locally available products (LAP) were 8 and 5 times more likely to possess more knowledge (p < 0.01) on water quality as compared to others that used only LAP. Slight improvements in attitudes and practices for every unit increment in knowledge were observed (p < 0.05). This limited familiarity with water quality management could severely impede the growth of aquaculture, as well as the sustainable utilization of available water resources. Therefore, there is a need for more training and improvement of extension services among fish farming communities. Full article