An immunomagnetic separation (IMS) method was developed to detect Toxoplasma gondii in fresh waters by using the monoclonal antibody 4B6 targeting the sporocyst wall of T. gondii, Hammondia hammondi, Hammondia heydorni, and Neospora caninum. Water concentrates obtained by filtering 10- to 20-l samples samples were spiked with Toxoplasma oocysts, sonicated to release the sporocysts, and analyzed by IMS-4B6. Mean sporocyst recoveries were 74.5±5.3% in drinking water, 30.6±2.4 and 37.1±3.2% in surface waters, and 81.6±2.1% in IMS buffer. Then, this IMS method was integrated in a multistep procedure (i.e., filtration, IMS, immunofluorescence and autofluorescence) to detect Toxoplasma in unspiked and spiked water samples (10–30 l) of various qualities. Sporocyst recoveries ranged from 14.4 to 44.7% in drinking water samples spiked with 1–10 oocysts/l, and from 17.8 to 32.5% in surface water samples spiked with 10 oocysts/l. Sporocysts were not detected in 25 unspiked water samples. A sporocyst-like structure was seen in one of these unspiked samples, but its coccidian nature could not be proved by three polymerase chain reaction (PCR) methods targeting sequences of coccidian small and large subunit rRNA genes and Toxoplasma repetitive elements. In conclusion, IMS-4B6 is relevant for the detection of Toxoplasma in water generating small concentrates (<1ml). Due to 4B6 cross-reactions, a PCR would be useful to further characterize coccidian sporocysts found microscopically.