An attempt was made for carrying out nutrient audits, which includes the calculation of nutrient balance at micro (plot/field), meso (farm) and macro (district) level and evaluation of trends in nutrient mining/enrichment. A nutrient budget is an account of inputs and outputs of nutrients in an agricultural system. NUTrient MONitoring (NUTMON) is a multiscale approach that assesses the stocks and flows of N, P and K in a well defined geographical unit based on the inputs and outputs. The calculated nutrient balances at crop activity level indicated a negative balance for cereals and pulses while positive for most of the horticultural crops. Similarly the results showed a negative balance for N and K and positive for P at farm level. Soil nutrient pool has to offset the negative balance of N and K hence there will be an expected mining of nutrient from the soil reserve in the study area. The management options/policy interventions to mitigate this mining by manipulating all inputs and outputs in a judicious way with an integrated system approach are also discussed. A strategy was worked out for deriving the fertilizer prescription rate using Decision Support System for Integrated Fertilizer Recommendation (DSSIFER) for the soil fertility status of the individual PPU of all the selected farms. By assuming DSSIFER prescribed fertilizers are applied to the individual PPUs, nutrient balance was generated with NUTMON-Toolbox and the results tend to be positive. NUTMON-Toolbox coupled with the systems approach for fertilizer optimization, DSSIFER and Agro ecological zoning would serve the purpose of gaining insight into long-term effects of farm management on enhancing soil fertility and productivity.