Among all the malaria controlling measures, biological control of mosquito larvae may be the cheapest and easiest to implement. This study investigated baseline predation of immature mosquitoes by macroinvertebrate predators along the Mara River, determined the diversity of predators and mosquito larvae habitats and the range of their adaptive capacity to water physico-chemical parameters. Between July and August 2011, sampling sites (n=39) along the Mara River were selected and investigated for the presence of macroinvertebrate predators and mosquito larvae. The selected sampling sites were geocoded and each dipped 20 times using standard mosquito larvae dipper to sample mosquito larvae, while a D-frame dip net was used to capture the macroinvertebrate predators. Water physico-chemical parameters (dissolved oxygen, temperature, pH, conductivity, salinity and turbidity) were taken in situ at access points, while hardness and alkalinity were measured titrimetically. The influence of macroinvertebrate predator occurrence was correlated with mosquito larvae and water quality parameters using Generalized Linear Model (GLM). Predators (n=297) belonging to 3 orders of Hemiptera (54.2%), Odonata (22.9%) and Coleoptera (22.9%), and mosquito larvae (n=4001) belonging to 10 species, which included An.gambiae s.l (44.9%), Culex spp. (34.8%) and An. coustani complex (13.8%), An. maculipalpis (3.6%), An. phaorensis (1.2%), An. funestus group (0.5%), An. azaniae (0.4%), An. hamoni (0.3%), An. christyi (0.3%), An. ardensis (0.08%), An. faini (0.07%), An. sergentii (0.05%) and 0.05% of Aedes mosquito larvae which were not identified to species level, due to lack of an appropriate key, were captured from different habitats along the Mara river. It was established that invasion of habitats by the macroinvertebrate predators were partially driven by the presence of mosquito larvae (p < 0.001), and the prevailing water physico-chemical parameters (DO, temperature, and turbidity, p <0.001). Understanding abiotic and biotic factors which favour mosquitoes and macroinveterbrate co-occurrence may contribute to the control of malaria.