Population interactions among mosquitoes in the Culex vishnui subgroup, which are vectors of Japanese Encephalitis, and their natural enemies were studied in Pondicherry, India. We tested the hypothesis that the breakdown of interactions between the larvae and their natural enemies due to drought followed by rain was responsible for the sudden increase in the vector population above the threshold for disease transmission during the heavy rainy period. We randomly sampled mosquito larvae and their predators in different breeding habitats and subjected the mean densities of prey, predator, and mosquito larvae infected with parasites/pathogens to covariate analysis to understand the interaction between prey and their natural enemies in relation to environmental factors. In rice fields, neither prey nor predator showed any positive correlation with temperature, RH, or the number of rainy days. However, the pathogen/parasite of mosquito immatures showed a positive correlation with RH. Among the mosquito predators, notonectids exhibited a significant positive correlation with Cx. vishnui larvae. The parasitic Romanomermis iyengari and pathogenic Coelomomyces anopheliscus also showed positive correlations with immatures. No parasites and pathogens of mosquito larvae were recorded in shallow water pools (SWP) or cement tanks (CT) during the study period. Important predators recorded in SWP were notonectids, damselfly nymphs, Diplonychus indicus, and hydrophilids. Dragonfly nymphs, gerrids, and tadpole shrimps were recorded in CT. In CT, prey and their predators were positively correlated with RH and rainy days. In SWP, there was a highly significant correlation between prey, predators and environmental factors. We conclude that rice fields are a stable ecosystem where regular interaction occurs between larvae and their natural enemies and a sudden increase in mosquito populations is uncommon. In transient habitats, no such stability is present and they become more important as breeding habitats in terms of seasonality and number. Shallow water pools should be seriously considered for the control of these vectors.