Yeast communities were isolated from water and sediment samples of two unpolluted natural lakes, located inside Rio Doce State Park, and two rivers located outside of this Park in Southeastern Brazil. A total of 134 yeast isolates were obtained and identified as belonging to 36 species. The numbers of fecal coliforms and yeast species were higher in rivers than in lakes. The genus Candida had the highest number of species with the presence of opportunistic pathogens such as Candida krusei, C. tropicalis, C. guilliermondii and C. parapsilosis. Yeasts able to grow at 37 degrees C were tested in relation to their susceptibility to common used antifungal drugs. Yeast isolates (13%) were susceptible to ketoconazole, 79% to fluconazole, 31% to terbinafine and 78% of the strains were susceptible to amphotericin B. Seven isolates from different Candida species were resistant to all antifungals tested. The high number of fecal coliforms found in these aquatic environments and the presence of resistant yeast strains to common used antifungal drugs suggest that these environments can pose potential health risks for people utilizing the contaminated waters.