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Larval control of Anopheles mosquitoes has long been neglected in tropical Africa due to uncertainties about its impacts on incidence and prevalence of malaria. Population models of mosquitoes are a useful tool to provide qualitative and quantitative understandings of influences of larval interventions on malaria transmission. For these purposes, we develop a new modeling framework by conceiving a quantity of the total productivity in an area, which, in turn, can be partitioned into its constituent parts from individual habitats. Three scenarios of larval interventions were evaluated in relation to impacts on parasitological indicators of malaria transmission. Our results show that it is unnecessary to manage all aquatic habitats to obtain significant reductions in incidence and prevalence of malaria in situations of low and intermediate levels of transmission. We highlight that informed larval interventions featured by identifying and targeting prolific habitats can play a critical role in combating malaria in Africa.