Climate change can play important roles in the hydrological processes within watershed with ponds as the Best Management Practice (BMP). Unlike several other studies, this study integrated remote sensing technique with hydrological model to identify and simulate pond BMP. Limited studies have been carried out to evaluate pond BMP in relation to the climate change impacts on hydrology and water quality particularly in Mississippi watersheds. The objective of this study was to classify ponds on satellite imagery within the Big Sunflower River Watershed (BSRW) using Google Earth Engine (GEE) and incorporate this data with Soil and Water Assessment Tool (SWAT) model to evaluate future hydrological and water quality outputs. The SWAT model was calibrated and validated against streamflow (R2 and NSE values from 0.81 to 0.56) and sediment (R2 and NSE values from 0.91 to 0.40). Future climate data for the mid (2040–2060) and late (2079–2099) centuries were utilized to create climate change scenarios (e.g., RCP 4.5 and 8.5). Results of this study projected that the average annual flow and sediment load will increase by 26–46%, and 107-150% respectively by the late century compared to the baseline period (2002–2021). However, the projected sediment load with modified pond BMP data used in the SWAT model could decrease average annual sediment load by 44–46% under both RCP scenarios. Seasonal data analysis determined that spring, summer, and fall sediment loads were projected to decrease up to 42%, 52%, and 46% respectively under both RCP scenarios due to pond BMP. This study can be useful for the development of climate-smart management strategies in agricultural watersheds.