Control of aquatic-stage Anopheles is one of the oldest and most historically successful interventions to prevent malaria, but it has seen little application in Africa. Consequently, the ecology of immature afrotropical Anopheles has received insufficient attention. We therefore examined the population dynamics of African anopheline and culicine mosquitoes using operationally practicable techniques to examine the relative importance and availability of different larval habitats in an area of perennial malaria transmission in preparation for a pilot-scale larval control programme. The study was conducted in Mbita, a rural town on the shores of Lake Victoria in Western Kenya, over 20 months. Weekly larval surveys were conducted to identify the availability of stagnant water, habitat characteristics and larval densities. Adult mosquitoes were collected indoors at fortnightly intervals. Availability of aquatic habitats and abundance of mosquito larvae were directly correlated with rainfall. Adult mosquito densities followed similar patterns but with a time-lag of approximately 1 month. About 70% of all available habitats were man-made, half of them representing cement-lined pits. On average, 67% of all aquatic habitats on a given sampling date were colonized by Anopheles larvae, of which all identified morphologically were A. gambiae sensu lato. Natural and artificial habitats were equally productive over the study period and larval densities were positively correlated with presence of tufts of low vegetation and negatively with non-matted algal content. The permanence of a habitat had no significant influence on larval productivity. We conclude that A. gambiae is broadly distributed across a variety of habitat types, regardless of permanence. All potential breeding sites need to be considered as sources of malaria risk at any time of the year and exhaustively targeted in any larval control intervention.