Water quality plays a substantial role in maximizing fish productivity. Despite the efforts made by government to improve fish production, there are general complaints about the small size of fish produced in aquaculture systems. This study was conducted in order to assess the effect of water quality on aquaculture productivity in Ibanda District, Uganda. The specific objectives were to examine the status of water quality parameters (temperature, turbidity, pH, alkalinity, Ammonia content, hardness, Carbon dioxide content, and Iron content) and assess their effect on fish pond productivity. Using data from fish farmers and water samples taken from 25 restocked fish ponds in ten sub-counties, the study revealed that of the eight water quality parameters examined only four (average turbidity, alkalinity, hardness, and Carbon dioxide content) were within the acceptable ranges, while Ammonia content, temperature, pH, and Iron content were slightly outside the recommended ranges. In addition, the study revealed that water quality parameters such as temperature, pH, and Ammonia Carbon dioxide, and Iron content had a significant effect on the weight and size of both tilapia and catfish. The study concluded that certain water quality parameters have a detrimental effect on fish farming. There is a need to educate fish farmers on how to maintain water quality at suitable levels in order to improve fish farm productivity in Ibanda district.