Ecotechnologies have the potential to reduce the use of finite resources while providing a variety of co-benefits to society, though they often lack in market competitiveness. In this study, we investigate the sustainability of ecotechnologies for recovering carbon and nutrients, and demonstrate how a so-called “bottom-up” approach can serve as a decision-making instrument. Based on three case study catchments with a focus on domestic wastewater in Sweden and Poland, and on manure, grass and blackwater substrates in Finland, we apply a cost–benefit analysis (CBA) on system alternatives derived from a participatory process. After drawing on an initial systematic mapping of relevant ecotechnologies, the scope of the CBA is determined by stakeholder suggestions, namely in terms of the considered assessment criteria, the physical impacts and the utilised data. Thus, this CBA is rooted in a localised consideration of ecotechnologies rather than a centralised governmental approach to systems boundaries. The key advantage of applying such a bottom-up approach is that it has gone through a robust participatory selection process by local stakeholders, which provides more legitimacy to the decisions reached compared with traditional feasibility studies. Despite considering the revenues of the recovered products as well as the provision of the non-market goods CO₂ mitigation and reduced eutrophication, findings from this study indicate that the benefits of the considered ecotechnologies are often outweighed by their costs. Only anaerobic digestion of agricultural wastes appears to be economically feasible under the current conditions, highlighting that further efforts and incentives may be required to mainstream ecotechnologies.