BackgroundOver the last few decades, river ecosystem is highly modified through various anthropogenic activities which are resulted to alter ecosystem functions and services. This modified ecosystem rendering conducive environment to mosquitoes through various ecological links for the self-sustaining populations. However, deciphering the community assemblage of immature mosquitoes with reference to water quality at modified ecosystem is very essential to make suitable control measure to curtail mosquito populations. In order to understand how the water quality influences the larval density, habitat specificity and community assemblage of immature mosquito populations, a study was conducted at different ecosystems (urban, semi-urban and rural) along the Vaigai river. The physicochemical parameters such as pH, TDS, salinity, conductivity, turbidity, DO, were analyzed at each study site.ResultsOur results clearly revealed that Anopheline species were highly preferred to breed less polluted habitat than Culicine species. Community assemblage by Anopheline and Culicine mosquitoes were found to be higher at all the studies whilst community assemblage by Anopheline were maximum at rural and semi-urban sites. Among the Anopheline species, Anopheles subpictus able to breed at high polluted habitat, particularly higher turbid level (28.49 ± 2.18 NTU) than other Anopheles species. Cx. gelidus mostly breed at sewage disposal habitats with high salinity level (1.01 ± 0.08) whilst Cx. bitaeniorhynchus bred in only fresh water bodies particularly low turbid habitats (3.97 ± 0.40 NTU). Grouping of immature mosquitoes based on the habitat similarity, An. subpictus, Cx. vishnui, An. vagus, Cx. tritaeniorhynchus, Cx. gelidus and Cx. quinquefasciatus were able to breed in highly polluted habitats which are resulted fell in group A than group B mosquitoes. Cx. vishnui and An. subpictus have strong habitat similarity (0.96) and can able to share their habitats with more number of Anopheline and Culicine mosquitoes.ConclusionsFrom the study we concluded that, Cx. vishnui and An. subpictus were most prevalent species and strong habitats similarity along the Vaigai river basin. An. subpictus and An. vagus can adapt to breed in polluted habitats and this may be adequate to extend the vectorial capacity and disease outbreak along the Vaigai river basin.