Malaria has reemerged in tropical regions with rapid population growth and deforestation. The dynamics of malaria transmission in agricultural settlements of the Amazon have been poorly defined. We studied the spatial distribution of malaria incidence in Roraima, Brazil, using multi regression analysis on 12 parameters that described social, housing, and behavioral variables. Malaria cases were associated with the proximity of Anopheles darlingi breeding sites, the main vector in these areas. During the dry season, transmission was enhanced near a temporary river. Cases occurred throughout the year near fish-farming dams. Epidemiological models derived from urban or riverine malaria are probably inadequate for describing disease transmission in agricultural settlements, where cases are clustered near breeding sites, while the majority of the population remains unaffected. Identification of these areas, associated with residual insecticide spraying or surveillance, may considerably decrease the costs of control efforts.