Intermediate host snails of schistosomiasis were surveyed in this study to determine their abundance and distribution in the lake and land aquatic habitats of Lake Victoria basin of Kenya. Several sites were sampled at eight locations, both in the lake and on the land. The habitat and/or vegetation type (i.e. open water, hippo grass, hyacinth, ambatch trees, other vegetation, stream, swamp, pond, dam) of the sampled aquatic sites within the locations were also differentiated, water physicochemical parameters were determined, and the abundance of different species or taxa of phytoplankton and zooplankton were enumerated and correlated with the abundance of schistosomiasis snails in the sites. The results indicated significantly more Biomphalaria sudanica snails than Bulinus africanus snails in different physical habitats on land (Student's t‐test, P < 0.05), as well as in different locations on land (Student's t‐test, P = 0.026). Regression analyses revealed that several physicochemical parameters, including dissolved oxygen (R2 = −0.659; n = 8; P = 0.014), pH (R2 = 0.728; n = 8; P = 0.007) and turbulence (R2 = −0.616; n = 8; P = 0.02), were predictive of Biomphalaria spp. abundance, while pH (R2 = 0.610; n = 8; P = 0.02) and turbulence (R2 = −0.578; n = 8; P = 0.028) were predictive of Bulinusspp. abundance in different locations in the lake. Cyanobacteria (R2 = 0.638; n = 8; P = 0.02) and chlorophyceae (R2 = −0.50; n = 8; P = 0.05) were shown to be predictive of both Biomphalaria spp. and Bulinus spp. abundance in different locations in the lake. Zooplankton abundance varied significantly between different locations in the lake (One‐way ANOVA, P < 0.001). Bosmina spp. were found to be predictive of both Biomphalaria spp. (R2 = −0.627; n = 8; P = 0.01) and Bulinus spp. (R2 = −0.50; n = 8; P = 0.05) in different locations in the lake. The results from this study will help inform policy regarding control measures for schistosomias and intermediate snail hosts in Lake Victoria waters, as well as in adjacent terrestrial aquatic habitats and even beyond.