In our study we analyzed the species composition of fungi and heterotrophic straminipiles in four ponds of a fish farm in Popielewo and in four ponds in Poryta Jabłoń situated in the vicinity of Knyszyn, Poland. Samples of water were collected during the spring and autumn of 2009. Fourty-two species (11 fungi and 31 heterotrophic straminipiles) were recovered. We found some potential pathogens of economically valuable fish and fish spawn, such as Achlya americana, Ac. polyandra, Saprolegnia ferax, and S. parasitica. In addition, we found some common human pathogens such as Aspergillus niger, and Candida tropicalis. Some saprotrophs such as Rhizophlyctis rosea, Nowakowskiella elegans, Olpidiopsis saprolegniae, Pythium debaryanum, Py. gracile, Py. hemmianum, and Py. inflatum appeared to be relatively common. Most species of fungi and straminipiles were recovered from ponds in Poryta Jabłoń (34), while the smallest number was found in Popielewo ponds (25). The physico-chemical analysis of water showed that ponds in Poryta Jabłoń were the least polluted with organic matter, whereas biogenic compounds were most abundant in Popielewo.