The occurrence and fate of surface water and wastewater pathogens (faecal coliforms, Escherichia coli, Giardia lamblia and Cryptosporidium parvum) in two constructed waterways and a pond-based AIT wastewater treatment plant (AIT WWTP) in Pathumthani, Thailand were studied in the context of several biogeochemical factors and in relation to pollutional pressure and seasonal phenomena with a view to proposing potential mechanisms for their removal. More data on pathogen removal in a given local context would provide assurance that some pathogens could serve as suitable indicator organisms and predict removal of different pathogenic microorganisms such as protozoan parasites covered in this study. The enumeration technique for protozoan pathogens was improved in terms of application of emerging novel molecular technologies for the development of a fast but affordable microbiological method. Potential risk of waterborne disease outbreak in pertinent communities was then characterized using established infection probability models and the compiled pathogen occurrence data. Overall, we have addressed several strategic priorities of pathogen research in waste stabilization ponds in developing tropical countries like