Although well-known methods for the detection of intestinal parasitic protozoans in water samples exist, they are insufficiently sensitive, expensive, of little practical value in the routine monitoring of waterborne pathogens and time- and labour-consuming. In the investigation reported here we have assessed Cryptosporidium oocyst detection using both the so-called Method 1623[recommended by the U.S. Environmental Protection Agency (USEPA)] and a direct method involving the determination of oocysts of Cryptosporidium in rotifers as detection tools of surface water contamination by dispersive stages of intestinal protozoans. Rotifers were sampled from three lakes located near the city of Poznan (Poland). To detect the oocysts of Cryptosporidium, we applied the fluorescent in situ hybridisation technique, an immunofluorescent assay and an enzyme immunoassay. Oocysts of Cryptosporidium were detected both in water collected from the lakes and in rotifers. The FISH technique applied to rotifers enabled the detection of biological contamination of surface water through an assessment of the dispersive stages of the parasite and was found to be more sensitive, less time-consuming and cheaper than the method recommended by the USEPA.