Estimation of hydrological processes is critical to water resource management, water supply planning, ecological protection, and climate change impact assessment. Mountains in Central Asia are the major source of water for rivers and agricultural practices. The disturbance of mountain forests in the region has altered the hydrological processes and accelerated soil erosion, mudflow, landslides, and flooding. We used the SWAT (Soil and Water Assessment Tool) model calibrated and validated with remote sensing data to quantify the mountainous hydrological processes in the Aktash River watershed (ARW) of Uzbekistan, Central Asia. Simulations showed that the daily surface runoff and streamflow closely responded to daily precipitation. Groundwater discharge reached its maximum in winter because of snowmelt. The wet months were from July to December, and the dry months were from January to June. The magnitudes of the seasonal hydrological processes were in the following order: fall > summer > winter > spring for precipitation and surface runoff; summer > spring > fall > winter for evapotranspiration (ET); winter > spring > fall > summer for snowmelt; fall > winter > summer > spring for water yield and streamflow; and winter > fall > spring > summer for groundwater discharge. The Mann–Kendall statistical test revealed a significant increasing trend for the annual precipitation (τ = 0.45, p < 0.01) and surface runoff (τ = 0.41, p < 0.02) over the past 17 years from 2003 to 2019. Compared to rangeland, forested land decreased monthly and annual average surface runoff by 20%, and increased monthly and annual average groundwater recharge by about 5%. Agricultural land had much higher unit-area values (mm/km2/y) of ET, groundwater recharge, and water yield than those of urban, forest, and range lands. Our research findings provide useful information to farmers, foresters, and decision makers for better water resource management in the ARW, Central Asia, and other mountain watersheds with similar conditions.