Intraguild predation (IGP) is common in the freshwater insect communities, involving a top predator, intraguild prey (IG prey) and a shared prey. Influence of the habitat complexity on the prey-predator interactions is well established through several studies. In the present instance, the IGP involving the heteropteran predators and the dipteran prey were assessed in the background of the habitat complexity. The three predators Diplonychus rusticus, Ranatra filiformis, and Laccotrephes griseus, one intraguild prey Anisops bouvieri and two dipteran prey Culex quinquefasciatus and Chironomus sp. were used in different relative density against the complex habitat conditions to deduce the impact on the mortality on the prey. In comparison to the open conditions, the presence of the macrophytes and pebbles reduced the mortality of the shared prey under intraguild system as well as single predator system. The mortality of the shared prey was however dependent on the density of the predator and prey. Considering the shared prey mortality, predation on mosquito larvae was always higher in single predator system than chironomid larvae irrespective of identity and density of predators. However, for both the shared prey, complexity of habitat reduced the prey vulnerability in comparison to the simple habitat condition. Higher observed prey consumption depicts the higher risk to predation of shared prey, though the values varied with habitat conditions. Mortality of IG prey (A. bouvieri) in IGP system followed the opposite trend of the shared prey. The lower mortality in simple habitat and higher mortality in complex habitat conditions was observed for the IG prey, irrespective of shared prey and predator density. In IGP system, the shared prey mortality was influenced by the habitat conditions, with more complex habitat reducing the vulnerability of the shared prey and increased mortality of the IG prey. This implies that the regulation of the mosquitoes, in the IGP system will be impeded by the habitat conditions, with the heteropteran predators as the top predator.