The present study is an evidence that depicts the degradation of agricultural yield in terms of soil nutrient (NH₄, NO₃, NO₂) deficit over 35 years (1979–2014) due to river sedimentation process within a small-scale basin. Literatures showed a significant decline in amount of nutrients from croplands in each year. In best of our knowledge, no such studies till date have examined small river basin environment to understand this inverse relationship between sedimentation process and soil nutrient loss using open source earth observation (EO) data and hydrological modelling at Indian context. SWAT model was applied to evaluate the basin hydrology and sedimentation process and associated soil nutrient conditions over time using historical flow and long-term meteorological data. Simulated sediment import and export significantly correlates (p < 0.00) with annual discharge values with the R² of 0.93 and 0.99 respectively. However, over the time different nutrient contents of soil such as NH₄, NO₃ etc. decreased drastically. Output reviles that NO₃ decreased from 32660 kg N to 5689 kg N within the observation period. Similarly, NH₄, and NO₂ also reduced with the 12020 kg N to 1577 kg N and 49.44 kg N to 6.85 kg N respectively. Total nitrogen and mineral phosphorus concentration also decreased over time. The Overall scenario showed that within 35 years, the increasing rate of sedimentation process through Gandheshwari river, adversely impact the agricultural yield concentration of the region. This study will help stakeholders, farmers to plan appropriate agricultural strategies at grass root level for small basin areas.