We investigated the role of heavy rain on container-inhabiting mosquito (Diptera: Culicidae) populations, and how different species may have adapted to such conditions. Rains were created with a rain simulator calibrated to natural rain intensities in the habitats of two important vector species: Aedes aegypti (L.) from northern Thailand and Culex pipiens L. from New York state, USA. Immature stages of Ae. aegypti were able to resist the flushing effect of rain better than Cx. pipiens. This difference was most dramatic during the pupal stage. Fourth instars of Ae. aegypti were not affected by flushing when exposed for longer rain intervals (30 versus 60 min) or at a colder water temperature (24 versus 16°C). In contrast, significantly more Cx. pipiens larvae flushed out with longer rain exposure. Warmer water temperatures also increased the proportion of Cx. pipiens flushed out, but mostly at the longest exposure time. Container position (tilted at a 7° angle or level) did not affect proportions of fourth instars flushed out for both species. More accurate models of vector-borne diseases can be developed by incorporating the described effects of rain on container-breeding mosquito populations. Such models may provide more realistic assessments of disease risk and ensure optimal use of limited financial resources of mosquito control agencies.