The Estonian concept of ecological networks (the Green Network) is implemented at different administrative levels by including multiple stakeholders. Building ecologically coherent Green Infrastructure is also one strategic aim of the European Union’s environmental policy. An embedded case study shows that contradictions between governance levels and ineffective stakeholder involvement measures have caused negative influence on land use decision-making processes on a local level. We further identified that the process of integrating the ecological network concept into the land use planning system has characteristics of vertical decentralisation, but the lack of relevant coordination have precluded achieving satisfactory results regarding stakeholder involvement and co-operation.