Abstract— A challenge of linking agricultural sector with water quality in order to combat water pollution remains worrying for the Government of Rwanda. The general objective of the study was to assess the potential impacts of agricultural practices on water quality in NYANZA District. Specifically, the study assessed agricultural practices in Bishya wetland, analyzed the level of water pollution in Bishya wetland, and demonstrated the correlation between agricultural practices and water quality from Bishya wetland. Data were obtained through questionnaires, observation, and laboratory analysis of water samples taken twice per month in six sampling points of bishya dam situated in bishya wetland starting from 4th March 2019 up to 20th August 2019. The Linear Regression Model using SPSS statistics with 95% confidence interval was used to demonstrate the correlation between agricultural inputs and water quality data for all selected physico-chemical parameters. Findings revealed that agricultural practices in Bishya wetland and surrounding areas are characterized by the presence of different crops, ineffective anti-erosions, absence of wetland margins, ineffective drainage of wetland, use of organic manures and chemical fertilizers, as well as the presence of different types of rocks and soils. Findings revealed also that all parameters have not manifested pollution, but some of them did according to Rwanda Standard Board guidelines. In sampling point1, the parameters that presented pollution were nitrites (r=0.047), phosphates(r=0.384), iron (r=0.11), and manganese(r=0.018); in sampling point2, were nitrites(r =0.010), iron (r=0.059), and chemical oxygen demand(r=0.012); in sampling point 3, were pH (r=0.048), nitrites(r =0.086), and phosphates (r=0.329); in sampling point 4, were nitrites (r =0.123), iron(r=0.182), and manganese (r=0.051); in sampling point 5,were turbidity (r=0.080), nitrites (r=0.095), phosphates(r=0.188),iron(r=0.093), manganese(r=0.051), and chemical oxygen demand(r=0.017), and in sampling point 6, the parameters that presented pollution were nitrites(r=0.046), phosphates(r=0.277), iron(r=0.106), and manganese(r=0.190). Finally, findings revealed that agricultural practices in Bishya wetland and surrounding areas, have contributed to the pollution of water quality of Bishya dam through substances of organic manures, chemical fertilizers and pesticides, crop residues, and soil sediments that are transported into the dam by erosion. The study concluded that an effort to create anti-erosions in all areas surrounding wetland, respectful of buffer zones, improving vegetation covers, creating water management bodies at cells level, increasing awareness of population about ecosystem functions, and capturing rain water from houses may effectively contribute to water quality in Bishya wetland.