This work aimed to analyse the water quality and identify the fungal diversity present in the skin and gills of tambatinga fish from the environmental protection area of the western lowlands of Maranhão, Brazil. The physicochemical parameters of water were analysed and microbiological tests were carried out to identify the most probable number of total coliforms and Escherichia coli. Forty tambatinga specimens were collected. In addition, skin and gill fragments were removed for fungi isolation in culture medium (BDA). Physicochemical and microbiological parameters of water, fish biometry and fungal diversity of fish in the dry and rainy periods were analysed.Results showed significant differences in the total length (TC) and weight (P) of fish in the dry and rainy periods. Microbiological data showed that the water of the four fish farms analysed in both periods are within the limits established by the National Environment Council (CONAMA) of Brazil and within limits established in complementary literature. Regarding the physicochemical parameters of water, only conductivity (F (1, 14) = 8.611; p = 0.011) and temperature had considerable differences (F (1, 14) = 11.037; p = 0.005). There was prevalence of yeasts (33%) and fungi of the genus Fusarium sp. (26%), Penicillium sp. (21%) and Aspegillus sp. (20%). The analysis of fungal diversity showed associations for sex, Aspegillus sp. (X2 = 19,600; DF = 1; p = 0,001) and the dry season, Penicillium sp. (X2 = 8,120; DF = 1; p = 0,004) and Fusarium sp. (X2 = 21.583; GL = 1; p = 0.001). It is concluded, therefore, that the harvests are within the established by the legislation of the National Environment Council-CONAMA in Brazil and complementary literature. However, it is necessary to evaluate the presence of possible mycotoxins in cultivated fish, since the most prevalent fungal species are considered to be mycotoxigenic fungi and are widely disseminated in the environment.