Understanding the trends in land use and land cover (LULC) is crucial for modeling streamflow and sediment yield, particularly in hydrological basins. This study examined the impact of LULC on the dynamics of streamflow and sediment yield within a humid tropical basin of the Atlantic Forest biome in Brazil, focusing on the period from 2000 to 2016. Changes in LULC were analyzed using annual MapBiomas data products for the same period. The Soil and Water Assessment Tool (SWAT) model was deployed to simulate streamflow and sediment yield based on LULC changes. To investigate temporal trends in LULC, a suite of non-parametric statistical tests, including the Mann–Kendall, Pettitt, and Sen’s slope estimator tests, was employed. Ecological diversity indices such as Shannon–Weaver, Simpson, and Pielou were applied to assess forest fragmentation, along with the Forest Fragmentation Index. The results revealed a growing trend in urban and sugarcane areas, coupled with a decline in dense vegetation, mangroves, and other forms of dense vegetation. With regard to the correlation between land uses and hydrological variables, the findings indicate minor variations in hydrological balance, attributable to the not-so-significant changes among the studied land-use scenarios, except for sediment yield estimates, which showed more considerable alterations. Notably, the estimates for 2000 and 2013–2016 were the most divergent. In a broader scientific context, this research conclusively establishes that the incorporation of dynamic LULC data into the SWAT model augments the precision and robustness of simulations pertaining to agricultural watersheds, thereby enabling a more comprehensive hydrological characterization of the study area.