In many regions across the planet, flood events are now more frequent and intense because of climate change and improper land use, resulting in risks to the population. However, the procedures to accurately determine the areas at risk in regions influenced by inadequate land uses are still inefficient. In rural watersheds, inadequate uses occur when actual uses deviate from land capability, and are termed environmental land use conflicts. To overcome the difficulty to evaluate flood vulnerability under these settings, in this study a method was developed to delineate flood vulnerability areas in a land use conflict landscape: the Batatais municipality, located in the State of São Paulo, Brazil. The method and its implementation resorted to remote sensed data, geographic information systems and geo-processing. Satellite images and their processing provided data for environmental factors such as altitude, land use, slope, and soil class in the study area. The importance of each factor for flood vulnerability was evaluated through the analytical hierarchy process (AHP). According to the results, vast areas of medium to high flood vulnerability are located in agricultural lands affected by environmental land use conflicts. In these areas, amplified flood intensities, soil erosion, crop productivity loss and stream water deterioration are expected. The coverage of Batatais SP municipality by these vulnerable areas is so extensive (60%) that preventive and recovery measures were proposed in the context of a land consolidation–water management plan aiming flood control and soil and water conservation.