Traditional solutions to estuarine flood risk management have typically involved the implementation of static 'hard' shoreline protection structures, often at the expense of the natural landscape and the societal and ecosystem benefits they provide. In a changing climate, there is an increasing need to restore these estuarine ecosystems, and alternative measures in the form of Nature-based Solutions (NbS) are being considered. Guidance that balances ecology and engineering is required for NbS to establish as self-sustaining ecosystems. In this study, a review of NbS guidelines was undertaken, revealing an absence of technical content bridging ecological and engineering values. Instead, most guidelines focus on NbS project implementation, identifying engineering aspects, and providing frameworks for investors and project managers. Integration of technical engineering and ecological outcomes within NbS guidelines is needed. A conceptual approach for integrating eco-engineering aspects for estuarine ecosystems is proposed. This conceptual approach focuses on the critical thresholds and parameter relationships associated with establishment, growth, recovery and mortality, and functionality of estuarine NbS, in efforts to quantify changes in ecological development and flood risk mitigation services. The conceptual approach documents how the suggested relationships between parameters can be adopted by practitioners in the short-term, medium-term, and long-term. The application of this conceptual approach to multi-habitat restoration is explored, including lifecycle timing and ecosystem/design functionality. The findings of this study demonstrate the need for an integrated NbS design guideline that balances ecology and engineering research for the long-term success of estuarine ecosystems.