The Khanikhola watershed in Sikkim is agrarian with about 50% area under rain-fed agriculture representing the conditions of the middle mountains all over the Himalaya. The study was conducted to assess overland flow, soil loss and subsequent nutrient losses from different land uses in the watershed, and identify biotechnological inputs for management of mountain farming systems. Overland flow, soil and nutrient losses were very high from open agricultural (cropped) fields compared to other land uses, and more than 72% of nutrient losses were attributable to agriculture land use. Forests and large cardamom agroforestry conserved more soil compared to other land uses. Interventions, like cultivation of broom grass upon terrace risers, N2-fixing Albizia trees for maintenance of soil fertility and plantation of horticulture trees, have reduced the soil loss (by 22%). Soil and water conservation values (> 80%) of both large cardamom and broom grass were higher compared to other crops. Use of N2-fixing Albizia tree in large cardamom agroforestry and croplands contributed to soil fertility, and increased productivity and yield. Bio-composting of farm resources ensured increase in nutrient availability specially phosphorus in cropped areas. Agricultural practices in mountain areas should be strengthened with more agroforestry components, and cash crops like large cardamom and broom grass in agroforestry provide high economic return and are hydroecologically sustainable.