Abstract Freshwater molluscs are hosts for diverse metazoan symbionts. However, apart from the digenean helminths, symbionts of molluscs are underreported worldwide. Therefore, this study focused on the diversity of oligochaetes, leeches, mites, insect larvae and nematodes associated with gastropods and bivalves from Lake Victoria, East Africa. Overall, 1,633 mollusc specimens representing 14 species were sampled from the Kenyan part of the lake. Each host specimen was examined to determine co‐occurrence of symbionts (including digeneans) and other metazoan invertebrates, and their microhabitat preferences on/in the hosts. In addition, prevalence and abundance of symbionts were compared for molluscs obtained from an unpolluted site, and sites that are eutrophic and polluted with heavy metals. In total, 33 species were recovered from the molluscs: six oligochaetes, four insects, two mites, two nematodes, one leech and 18 digeneans. The nematode Daubaylia potomaca, mite Unionicola macani, leech Batracobdelloides sp., oligochaetes Chaetogaster limnaei, Dero digitata, Aulophorus africanus, Allonais paraguayensis and Ophidonais serpentina, and gorgoderid digenean larvae are new records for Lake Victoria. Moreover, the genus Bratislavia (Oligochaeta) is reported for the first time in Africa. Our results show that parasitic mites and leeches were absent from mollusc specimens that harboured chironomids. Likewise, there was no co‐occurrence of C. limnaei, D. potomaca and digeneans, suggesting that antagonistic interactions occur between the symbionts. Although co‐occurrence of mites and digeneans in individual mollusc hosts was common, the symbionts occupied different microhabitats. This study shows that prevalence and intensities of U. macani and C. limnaei, were significantly higher in hosts from the unpolluted site, compared with the polluted sites. What is more, D. potomaca and trichopteran larvae, were recorded only from the unpolluted site. The distribution of the chironomid Kiefferulus chloronatus suggests their preference for sites that are rich in organic matter and their ability to tolerate pollution. Information on antagonistic interactions between symbionts might be applicable in biocontrol, especially of digenean species that have veterinary or medical importance. Finally, this study shows a potential for the use of U. macani, C. limnaei, D. potomaca and insect larvae as discriminators of the quality of aquatic habitats.