We performed bimonthly mosquito larval collections during 1 year, in an agricultural settlement in the Brazilian Amazon, as well as an analysis of malaria incidence in neighboring houses. Water collections located at forest fringes were more commonly positive for Anopheles darlingi larvae and Kulldorff spatial analysis pinpointed significant larval clusters at sites directly beneath forest fringes, which were called larval “hotspots.” Remote sensing identified 43 “potential” hotspots. Sampling of these areas revealed an 85.7% positivity rate for A. darlingi larvae. Malaria was correlated with shorter distances to potential hotpots and settlers living within 400 m of potential hotspots had a 2.60 higher risk of malaria. Recently arrived settlers, usually located closer to the tip of the triangularly shaped deforestation imprints of side roads, may be more exposed to malaria due to their proximity to the forest fringe. As deforestation progresses, transmission decreases. However, forest remnants inside deforested areas conferred an increased risk of malaria. We propose a model for explaining frontier malaria in the Amazon: because of adaptation of A. darlingi to the forest fringe ecotone, humans are exposed to an increased transmission risk when in proximity to these areas, especially when small dams are created on naturally running water collections.