This study investigates the impact of climate on the variation of pathogenic bacteria in the Manathira River. A spatial and temporal analysis of bacterial populations in relation to environmental factors was conducted. The results highlight substantial spatial differences in bacterial counts, with elevated levels near urban and agricultural areas. Bacterial counts decrease with distance from these sources. Furthermore, a clear seasonal trend is observed, with higher counts during the spring and fall, likely due to climatic conditions favoring bacterial growth. Importantly, all identified bacterial species present health risks to humans, animals, and plants. This study underscores the importance of monitoring and managing bacterial contamination in the Manathira River to safeguard public and environmental health.