Wetland ecosystems are unique ecologically and incessant human dependence is noted from time immemorial. Water rats (Rattus norvegicus) play a vital role in disease transmission and a study was conducted to assess the pathogenic diversity among water rats (Rattus norvegicus) inhabiting Vembanadu-Kol wetland agroecosystem. A total of twelve bacterial pathogens were isolated from the trapped six water rats including Salmonella enterica, Klebsiella pneumoniae and Staphylococcus aureus. Fifteen fungal pathogens were isolated including two dermatophytes (Microsporum audouinii and Trichophyton rubrum). Genus Aspergillus was more predominant representing four species. The presence of Trichosoporon biegelii was observed in both blood and lungs. Six parasites were also identified with more prevalence of Ancylostoma duodenalae (100%) followed by Hymenolepis diminuta (66.67%). As human-water-rat contact is inevitable in wetland ecosystem, the presence of pathogens in rats inhabiting in it are a matter of serious concern.