The goal of this study was to standardise and use parasitological and molecular techniques in the analysis and seasonal monitoring of opportunistic protozoa in water from fluvial systems for human usage in the municipality of Goiânia, the capital of the state of Goiás, in the midwestern region of Brazil. We focused on Cryptosporidium sp. Cyclospora cayetanensis, Isopora belli, Microsporidia and Giardia lamblia. Water samples were collected monthly from February 2006 to January 2007 and concentrated using vacuum filtration and a positively charged membrane. Several methods were used to identify the different protozoa of interest. To detect coccidia (Cryptosporidium sp., Isospora belli, and Cyclospora cayetanensis), we used a Kinyoun hotstaining method and a modified Ziehl-Neelsen technique. Enteral microsporidia were detected by a hot-chromotrope technique while a MERIFLUOR ® Cryptosporidium kit was used to confirm the presence of Cryptosporidium sp. Finally, we used PCR to detect Cryptosporidium parvum/hominis. Water is of vital importance to living beings; however, due to anthropic action, several microorganisms are disseminated into aquatic environments. Among them are opportunistic protozoa that infect mainly immunodepressed and immunosuppressed individuals, children and elderly people. These protozoa pose a significant health hazard. Nevertheless, the presence of these pathogens is underestimated because they are not considered during routine environmental monitoring. In our study, we were able to observe the presence of Giardia cysts, Cryptosporidium sp. and Cryptosporidium parvum oocysts in the bodies of water monitored in this research.