Changes in land use can cause degradation of soil physical quality with negative effects on the environment and agricultural production. The effects of different land uses on soil physical-hydric attributes were studied in the Renato River and Caiabi River watersheds in the southern Brazilian Amazon. Three conditions of land use were evaluated: native forest, crops, and pasture in the headwater, middle, and mouth of each watershed. Particle size, particle density, bulk density, total porosity, macroporosity, microporosity, water contents at field capacity and permanent wilting point, and available water capacity in soil were evaluated in three soil layers down to 0.4 m. Data collected were subjected to the Kruskal–Wallis nonparametric test and Pearson’s correlations. Multivariate analyses were also performed using the principal component method. In the Renato watershed, in comparison with native forest, conventional management of pasture and crops caused soil physical degradation, increasing soil density in the surface layer and reducing macroporosity and total porosity. In the Caiabi watershed, converting native forest areas into pasture and crops altered water quality, influencing the water dynamics in the soil, by reducing soil water conductivity. Soil attributes varied by watershed, with texture variations between the headwater and mouth, indicating that changes in soil properties result from both management and the granulometric composition of the soil in different regions of the same watershed. Adoption of crop and pasture conservation practices can improve soil physical attributes in regions bordering agricultural areas in the southern Amazon.