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Studies on the impacts of land-use and land-cover change on stream hydrochemistry in active deforestation zones of the Amazon agricultural frontier are limited and have often used low-temporal-resolution datasets. Moreover, these impacts are not concurrently assessed in well-established agricultural areas and new deforestations hotspots. We aimed to identify these impacts using an experimental setup to collect high-temporal-resolution hydrological and hydrochemical data in two pairs of low-order streams in catchments under contrasting land use and land cover (native vegetation vs. pasture) in the Amazon and Cerrado biomes. Our results indicate that the conversion of natural landscapes to pastures increases carbon and nutrient fluxes via streamflow in both biomes. These changes were the greatest in total inorganic carbon in the Amazon and in potassium in the Cerrado, representing a 5.0- and 5.5-fold increase in the fluxes of each biome, respectively. We found that stormflow, which is often neglected in studies on stream hydrochemistry in the tropics, plays a substantial role in the carbon and nutrient fluxes, especially in the Amazon biome, as its contributions to hydrochemical fluxes are mostly greater than the volumetric contribution to the total streamflow. These findings demonstrate that assessments of the impacts of deforestation in the Amazon and Cerrado biomes should also take into account rapid hydrological pathways; however, this can only be achieved through collection of high-temporal-resolution data.