The abundance of mosquito larvae in relation to associated microbiota and physicochemical parameters of water in marshes from selected habitats in Kelaniya divisional secretariat area, of the Gampaha district, Sri Lanka were studied. Culex gelidus was found to be the dominant mosquito species found in marshes followed by Culex whitmorei, Culex tritaeniorhynchus, Culex quinquefasciatus, Culex fuscocephala, and Anopheles peytoni. Fourteen species/taxa of microbiota were identified. There was a significant positive correlation between the abundance of Cx. gelidus larvae and level of organic pollution in marshes as measured by the five-day Biological Oxygen Demand. A positive correlation for the presence of Cx. fuscocephala and Cx. gelidus in the marshland was also observed. Nevertheless, abundance of Cx. gelidus was negatively correlated with Cx. quinquefasciatus and Cx. whitmorei. The presence of Culex gelidus and Cx. tritaeniorhynchus were positively correlated with Daphnia magna indicating their co-existence in the same habitat requirement. Culex gelidus was negatively affected by the epibiont, Vorticella microstoma, when the latter organisms were present in higher densities. In contrast, the presence of Cx. whitmorei was positively influenced by the Vorticella microstoma, Difflugia corona, nauplius larva, and Keratella valga. There was a negative correlation between Cx. whitmorei and Monostyla bulla (Rotifera; Monogononta) and between the abundance of Cx. fuscocephala and Lecane luna in the same marshland. This study concludes that mosquito larvae and some microbiota are interdependent in marshlands. The level of abundance of mosquito larvae and microbiota varied with the level of water pollution. Cx. gelidus larvae are biologically affected by Vorticella microstoma. Many microbiota species compete with mosquito larvae for the same food items.