The SOWAP organisation reflects the complex inter-relationships in this multi-stakeholder, multi-disciplinary project. SOWAP is led by an overall project manager. Each country has its own organisational structure, with a country manager reporting to the overall project manager. The country managers are responsible for co-ordinating SOWAP activities and delivering its objectives in their respective countries.

A ‘pan-European lead' defines the activities within each area of work e.g. soil, biodiversity, to ensure technical excellence and consistency across the project. These activities are co-ordinated by ‘country leads' in each country. Timelines and plans for the areas of work are agreed between Pan-European leads and country leads and submitted to the SOWAP project manager for approval. Individuals responsible for undertaking the work will report to the country leads.