The Brazilian Cerrado is recognized as one of the most threatened biomes in the world, as the region has experienced a striking change from natural Cerrado vegetation to intense cash crop production. This paper reviews the history of land conversion in the Cerrado and the development of soil properties and water resources under past and ongoing land use. We compared soil and water quality parameters from different land uses considering 80 soil and 18 water studies conducted in different regions across the Cerrado to provide quantitative evidence of soil and water alterations from land use change. Following the conversion of native Cerrado, significant effects on soil pH, bulk density and available P and K for croplands and less-pronounced effects on pastures were evident. Soil total N did not differ between land uses because most of the sites classified as croplands were nitrogen-fixing soybeans, which are not artificially fertilized with N. In contrast, water quality studies showed nitrogen enrichment in agricultural catchments, indicating fertilizer impacts and potential susceptibility to eutrophication. Regardless of the land use, P is widely absent because of the high-fixing capacities of deeply weathered soils and the filtering capacity of riparian vegetation. Pesticides, however, were consistently detected throughout the entire aquatic system. In several case studies, extremely high-peak concentrations exceeded Brazilian and European Union (EU) water quality limits, which were potentially accompanied by serious health implications. Land use intensification is likely to continue, particularly in regions where less annual rainfall and severe droughts are projected in the northeastern and western Cerrado. Thus, the leaching risk and displacement of agrochemicals are expected to increase, particularly because the current legislation has caused a reduction in riparian vegetation. We conclude that land use intensification is likely to seriously limit the Cerrado's future regarding both agricultural productivity and ecosystem stability. Because only limited data are available, we recommend further field studies to understand the interaction between terrestrial and aquatic systems. This study may serve as a valuable database for integrated modelling to investigate the impact of land use and climate change on soil and water resources and to test and develop mitigation measures for the Cerrado.