The aim of the study is to assess climate-smart water management practices for sustainable agriculture in the Lake Mutanda catchment area, Kisoro District, Uganda. The study was led by specific objectives, specifically: assessing the effects of flooding on agricultural productivity, and smallholder farmer's responses to rainfall variability for the past 20–30 years, investigating climate-smart water management practices for sustainable agriculture, and analyzing the seasonal variations of the physicochemical water quality parameters. The study used a mixed research design, which used mixed methodologies to collect and analyze data using both quantitative and qualitative approaches. A straightforward random sampling approach was used to determine the sample size. Three hundred and ninety-seven respondents participated in the study. Quantitative data was analyzed using the R programming language, and qualitative data was analyzed using ATLAS.ti. The study identified climate-smart water management practices like mulching, terracing, contour farming, conservation tillage, agroforestry, and fertilizer management. Most of the respondents (29.7%) cited a reduction in soil fertility. 57.9% of the total sampled respondents had noticed changes in rainfall variability, and 67.3% reported a decrease in rainfall. The majority (38% of the participants) use mulching to reduce running water into the catchment areas. Turbidity, temperature, and DO were beyond the WHO-permitted levels.