Deforestation has been linked to a rise in malaria prevalence. In this paper, we studied longitudinally 20 spots, including forested and deforested portions of a temporary river in a malarigenous frontier zone. Larval habitat parameters influencing distribution of Anopheles darlingi (Diptera: Culicidae) larvae were studied. We observed that larvae were clustered in forested-deforested transitions. For the first time in the literature, it was verified that parameters determining larval distribution varied from deforested to forested areas. The proximity to human dwellings was also a significant factor determining distribution, but larvae was most importantly associated with a previously undescribed parameter, the presence of small obstructions to river flow, such as tree trunks within the river channel, which caused pooling of water during the dry season ('microdams'). In deforested areas, the most important factor determining distribution of larvae was shade (reduced luminance). Larvae were absent in the entire studied area during the wet season and present in most sites during the dry season. During the wet-dry transition, larvae were found sooner in areas with microdams, than in other areas, suggesting that flow obstruction prolongs the breeding season of An. darlingi. Adult mosquito densities and malaria incidence were higher during the dry season. Our data correlate well with the published literature, including the distribution of malaria cases near the forest fringes, and has permitted the creation of a model of An. darlingi breeding, where preference for sites with reduced luminance, human presence and microdams would interact to determine larval distribution.