Abstract Climate change has been a serious issue in many countries, including Uganda, and has led to water contamination, pollution, and even water scarcity. Wetlands have shown their capacity to maintain water quality and safety for the population’s health through their filtering function, but they are highly susceptible to agricultural activities and destruction. This study aimed to determine the status of fifteen wetlands in the Rukiga district and the impact of climate hazards and human activities on water quality in the area where a conservation project was implemented by three organisations. Eighteen-month records were obtained, and readings were taken to determine the turbidity level of the water from the different wetlands. The reading mean of each wetland was used to determine three water source categories: clear or non-turbid (read > 80), less turbid (read 50–80), and very turbid (read 0–50). Analysis was performed with SPSS V28.0, which included univariate and bivariate analyses. Observation and conversation notes with project staff and community members were taken. The study showed that 93.33% of the water sources from wetlands were turbid, and for some, the turbidity did not oscillate stably from one category to another. Only one water source (6.67%) was still clear (non-turbid) for 18 months. These communities mostly contain wetlands as the main sources of water, which is collected from streams. Wetlands are more susceptible to agricultural activities, and hills are deforested exposing to soil erosion leading to water contamination. In conclusion, most wetlands are destroyed and have lost their filtering capacity and exposing people to consumption of unsafe water. Climate hazards and agricultural activities contributed the most to this issue. Interactions between NGOs and communities are helpful in responding to this threat.