Environmental disturbances such as deforestation, urbanization or pollution have been widely acknowledged to play a key role in the emergence of many infectious diseases, including mosquito-borne viruses. However, we have little understanding of how habitat isolation affects the communities containing disease vectors. Here, we test the effects of habitat type and isolation on the colonization rates, species richness and abundances of mosquitoes and their aquatic predators in water-filled containers in northwestern Thailand. For eight weeks water-filled containers were monitored in areas containing forest, urban and agricultural habitats and mixtures of these three. Mosquito larvae of the genera Aedes and Culex appeared to be differentially affected by the presence of the dominant predator; Toxorhynchites splendens (Culicidae). Therefore, a predation experiment was conducted to determine predator response to prey density and its relative effects on different mosquito prey populations. Colonization rates, species richness and abundances of mosquito predators were strongly related to forest habitat and to the distance from other aquatic habitats. Areas with more tree cover had higher predator species richness and abundance in containers. Containers that were close to surface water were more rapidly colonized than those further away. In all habitat types, including urban areas, when predators were present, the number of mosquito larvae was much lower. Containers in urban areas closer to water-bodies, or with more canopy cover, had higher predator colonization rates and species richness. T. splendens (Culicidae) preyed on the larvae of two mosquito genera at different rates, which appeared to be related to prey behaviour. This study shows that anthropogenic landscape modification has an important effect on the natural biological control of mosquitoes. Vector control programmes and urban planning should attempt to integrate ecological theory when developing strategies to reduce mosquito populations. This would result in management strategies that are beneficial for both public health and biodiversity.