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 and reduced inputs. This was accompanied by a reduction of 30–35 % in atmospheric emissions of ammonia and nitrous oxide as well a decline in N and P runoff of 35 and 10 %, respectively, whereas the emission of methane increased with 4 %. Model results compared well with (i) large scale observations of ammonia concentrations in air and nitrate concentrations in upper groundwater and ditch water, (ii) with nitrous oxide emissions and phosphorus adsorption in experiments at field scale and (iii) with metal adsorption in large scale soil datasets. Various mitigation measures were evaluated in view of policy ambitions for climate, soil and environmental quality for 2030, i.e. a reduction of 50 % for NH3, 11–17 % for GHG, 20 % for N runoff and 40 % for P runoff and an ambition of 50 % GHG emission reduction for 2050. The measures focused on a combination of animal feeding, low emission housing and application technologies, improved crop, soil and nutrient management, all being applied with an effectiveness of 100 % and 50 %, respectively. In addition, we evaluated impacts of 50 % livestock reduction, and combination scenarios of measures and livestock reduction. Full implementation of all measures can reduce NH3 emission, N leaching and N runoff by approximately 40–50 % and GHG emissions by approximately 30 %, but there is less potential to reduce P runoff, being <10 %. The combination of a more likely 50 % implementation/effectiveness of measures with 25 % livestock reduction leads to a comparable reduction. Required reductions from Dutch agriculture seem not possible with improved management only, but also requires livestock reduction, especially when the NH3 ambitions at the short term (2030) and the climate ambitions for the long term (2050) should be attained.