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To gain insight in the environmental impacts of crop, soil and nutrient management, an integrated model framework INITIATOR was developed predicting: (i) emissions of ammonia (NH₃) and greenhouse gases (GHG) from agriculture, including animal husbandry and crop production and (ii) accumulation, leaching and runoff of carbon, nutrients (nitrogen, N, phosphorus, P, and base cations) and metals in or from soils to groundwater and surface water in the Netherlands. Key processes in soil are included by linear or non-linear process formulations to maintain transparency and to enable data availability for spatially explicit application from field up to national level. Calculated national trends in nutrient losses over 2000–2020 compared well with independent estimates and showed a reduction in N and P input of 26 to 33 %, whereas the surplus declined by 33 % for N and 86 % for P due to increased crop yields …