Based on the highest pre-identified risk of flooding in the Glinščica catchment, our case study focused on identifying the benefits and opportunities of ecosystem services emerging from fully functioning ecosystems working as a natural assurance system arising from Nature-based solutions (NBS) through the implementation of a participatory approach. Together with our stakeholders we first, developed an NBS strategy for the Glinščica catchment and compared it to the business as usual, second, evaluated the ecosystem services provided by the simulated implementation of restoration and management measures selected and third, developed economic and financial instruments in the form of natural assurance schemes based on effective business models in the field of ecosystem services, green infrastructure and river restoration. This highlighted the importance of understanding the value of ecosystems in the long term. The participatory process was basically an iterative process in which expert studies formed the basis for stakeholder engagement on the one hand and the stakeholders’ perceptions and knowledge were shaping and directing the solutions on the other hand. Stakeholders eventually agreed that the developed strategy for water risk mitigation using NBSs in the Glinščica catchment is a viable alternative to existing grey infrastructure plans. However, the participatory process revealed several barriers to mainstreaming NBS and implementing an adaptive management approach in Slovenia, mostly in the governing and institutional systems. Through the participatory planning process, we built capacity and changed the perceptions of participating stakeholders regarding NBSs and their efficiency in providing multiple co-benefits in addition to the flood protection, which is usually the only function and benefit of grey measures.