The protozoan parasite Toxoplasma gondii infects a large proportion of threatened California sea otters (Enhydra lutris nereis), and is an important waterborne pathogen in humans. Contamination of coastal waters with T. gondii is thought to occur through delivery of environmentally resistant oocysts to nearshore regions via overland runoff. The objectives of this study were to evaluate whether T. gondii oocysts and surrogate microspheres attach to aggregates ($ 0.5 mm), and whether the magnitude of aggregation depends on water type, specifically salinity. Laboratory aggregation studies were conducted by adding T. gondii oocysts and surrogate microspheres to riverine, estuarine, and marine waters, and quantifying the proportion of oocysts and surrogates in aggregate-rich and aggregate-free water fractions. Attachment of oocysts and surrogates to aggregates occurred in all water types, but was greater in estuarine and marine waters, with concentrations of T. gondii in aggregates enriched 3-4 orders of magnitude. Aquatic aggregates may, thus, significantly influence waterborne transport of terrestrially derived pathogens, both through enhanced settling and subsequent concentration in the benthos, as well as by facilitating ingestion by invertebrate vectors that can transmit pathogens to susceptible hosts, including sea otters and humans.