About 44% of the Indian landmass experiences the adverse impact of land degradation. This loss of sediments caused by soil erosion reduces the water quality of local water bodies and decreases agricultural land productivity. Therefore, decision-makers must formulate policies and management practices for sustainable management of basins that are cost-effective and environment friendly. Application of the best management practices (BMPs) to properly manage river basins is difficult and time-consuming. Its implication under various climate change scenarios makes it more complicated but necessary to achieve sustainable development. In this study, the soil and water assessment tool (SWAT) model was employed to prioritize the Tons river basin’s critical areas in the central Indian states coupled with future climate scenario analysis (2030–2050) using Representative Concentration Pathway (RCP) 4.5 and RCP 8.5 scenarios. The SWAT model was calibrated and validated for simulation of streamflow and sediment yield for daily and monthly scales using the sequential uncertainty fitting (SUFI-2) technique. The values of coefficient of determination ( R2), Nash–Sutcliffe efficiency (NSE), percent bias (PBIAS), and root mean square error (RMSE)-observations standard deviation ratio (RSR) were .71, .70, −8.3, and .54, respectively during the calibration period, whereas for validation the values were .72, .71, −3.9, and .56, respectively. SWAT model underestimated the discharge during calibration and overestimated the discharge during validation. Model simulations for sediment load exhibited a similar trend as streamflow simulation, where higher values are reported during August and September. The average annual sediment yield of the basin for the baseline period was 6.85 Mg ha−1, which might increase to 8.66 Mg ha−1 and 8.79 Mg ha−1 in the future years 2031–2050 and 2081–2099, respectively. The BMPs such as recharge structure, contour farming, filter strip 3 and 6 m, porous gully plugs, zero tillage, and conservation tillage operations have been considered to evaluate the soil and water conservation measures. Recharge structure appeared to be the most effective measure with a maximum reduction of sediment by 38.98% during the baseline period, and a 37.15% reduction in the future scenario. Sub-watersheds, namely SW-8, SW-10, SW-12, SW-13, SW-14, SW-17, SW-19, SW-21, SW-22, and SW-23, fall under the high category and are thus considered a critical prone area for the implementation and evaluation of BMPs. Compared to the baseline period, the effectiveness of BMPs is slightly decreasing in the 2040s, increasing in the 2070s and decreasing in the 2090s. Recharge structure and filter strip 6 m have been found to nullify the high soil erosion class completely. Overall, SWAT model simulations under the RCP 8.5 scenarios were observed to be reliable and can be adopted to identify critical areas for river basins having similar climatic and geographical conditions.