| Tool | Module | Inputs | Outputs |
| PCRaster | Grid layers of soil surface, soil, and subsoil; hydrological network | Annual rainfall, temperature, nitrogen inputs from soil surface surplus | Discharge, nitrogen fluxes |
| ExtendSim | Nitrogen production | Cattle density, crop area | Nitrogen surplus; dairy, meat, and crop production |
| Nitrogen abatement costs | Nitrogen norm, nitrogen surplus, production | Transport costs, processing costs | |
| Farm income | Cattle, transport costs, processing costs | Income per farm and per employee | |
| Income effect | Income per farm | Change in number of farms | |
| Farm area reallocation | Income per farm, number of farms, change in number of farms | Area per farm | |
| Source deposition standard | Nitrogen concentration | Nitrogen norm | |
| Estuarine box model | Upstream concentration, downstream concentration | Box concentration | |
| Climate change (generic scenario dialog) | Scenario 1990–2050 | Annual precipitation, mean temperature | |
| Policy measure option (generic module) | Start and end time, step size, path to input file | Various, e.g., cattle stock reduction, buffer strips, fertilizer use, nitrogen concentration at outflow point | |
| Spatial-dynamic interface (generic module) | Time step | N/A | |