Pathogenic fungi are a concern for both environmental and public health. Understanding the spatial distribution and the influence of environmental factors on the growth and proliferation of these fungi is crucial for effective management and mitigation strategies. This study presents a comprehensive spatial analysis of pathogenic fungi in the Manathira River, assessing their presence and abundance in relation to various environmental factors. The research involved extensive sampling and laboratory analysis of soil and water samples from multiple locations along the Manathira River throughout different seasons. Results revealed spatial and temporal variations in the growth of pathogenic fungi, with higher numbers during the spring and autumn seasons and lower counts during winter and summer. These fluctuations are attributed to the diverse climatic conditions experienced across the seasons. Furthermore, the study highlighted that the numbers of pathogenic fungi tend to increase in locations affected by residues from urban and agricultural activities. As one moves away from these sources, their numbers decrease. This finding underscores the importance of managing and mitigating environmental pollution to reduce the proliferation of pathogenic fungi in aquatic ecosystems. The research also identified new species of pathogenic fungi not previously documented in the Manathira River, including Mucoracemosus, Fusarium culmorum, and Paecilomyces sp. This discovery emphasizes the need for ongoing monitoring and research to better understand the dynamics of fungal communities in aquatic environments. In conclusion, this spatial analysis provides valuable insights into the environmental factors influencing the growth and proliferation of pathogenic fungi in the Manathira River. The findings can inform strategies for the sustainable management and protection of aquatic ecosystems, ultimately safeguarding both the environment and public health.