Our study involved the quantitative analysis of species composition of fungi and straminipilous organisms in four ponds situated in Białystok, Poland. The observations performed in April and November 2006 with respect to hydrochemical conditions revealed the occurrence of 48 species, including 9 fungi and 39 straminipilous organisms. Among species of fungi and straminipilous organisms, we found such pathogens of crustaceans and fish as Achlya dubia, Ac. oblongata, Ac. polyandra, Aphanomyces bosminae, Ap. laevis, Dictychus monosporus, Pythium jirovecii, Py. undulatum, Saprolegnia ferax, S. parasitica, S. pseudocrustosa and Thraustotheca clavata. The human pathogens Aspergillus niger, Candida tropicalis and Catenophlyctis variabilis as well as plant pathogens Pythium butleri and Py. debaryanum were also found. Such phytosaprophytes as Achlya klebsiana, Karlingia rosea, Nowakowskiella elegans, N. macrospora, Pythium akanense, Py. aquatile, Py. elongatum, Py. inflatum and Py. intermedium were relatively common. Most species of fungi and straminipilous organisms were found to grow in Dojlidy Pond (27), the fewest in Akcent Pond (14). The hydrochemical analysis of water showed that Dojlidy was the least burdened with organic matter, whereas Akcent was the most abundant in biogenic compounds.