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We quantified the effects of deforestation, and subsequent cultivation and forest regeneration, on the abundance and composition of mosquito larval habitats, specifically phytotelmata (plant-held waters), in the western Amazon basin. Recently deforested sites were characterized by increased phytotelm density (1.6 phytotelmata/m2) and greater relative abundance of fallen-plant-part phytotelmata (76%) compared to intact forests (0.9 phytotelmata/m2 and 25% fallen plant parts). As a result, the total volume of colonizable phytotelm water was significantly larger in new clearings. Subsequent cultivation of cleared land with mixed crops including pineapple and plantain had similar consequences: phytotelm density (2.2 units/m2) was significantly larger in plantations than in forests due to greater relative abundance of water-filled plant axils (71% vs. 39% in forest). Such axils are the preferred larval habitats for Wyeomyia spp. mosquitoes, which showed a similarly significant increase in production in plantations (0.25 larvae/m2) vs. forests (0.04 larvae/m2). Likewise, Limatus spp. mosquitoes were an order of magnitude more abundant in altered landscapes (especially in recently deforested and cultivated areas) than in mature forest, due to increased abundance of fallen-plant-part phytotelmata, in which they are typically the most common colonists. Because they are potential vectors of pathogens in a region of high endemic and emergent virus activity, increases in local abundance of Limatus spp. and Wyeomyia spp. due to large-scale deforestation and agriculture may influence rates of disease transmission.