A major challenge for the modern river and coastal management is a holistic design approach in order to integrate flood and erosion protection combined with ecological restoration. Nowadays, a lot of EU regulations request nature-based engineering solutions such as soil and water bioengineering techniques (SWBE). In contrast to conventional ‘hard’ civil engineering structures, the idea of SWBE structures is the use of biological components in the engineering structure to not just consider a technical function, but also ecological and aesthetic values. While SWBE techniques are applied worldwide and well established as an engineering discipline, there is a high demand on the further development specifically in terms of ecology.The use of plants in river engineering projects requires the right choice of species depending on the techniques used and the environmental conditions. Furthermore, a right harvest, storage and implementation of the plants is significant. Their use also requires the quantification of the hydraulic and sedimentological impact of riparian vegetation on the one hand and on the other hand to know the impact of SWBE structures on the aquatic and terrestrial habitats. Different ecological, vegetational and phytosociological criterias are available and discussed in terms of assessment of SWBE structures. All these criteria can be helpful to develop a framework supporting stakeholders to define objectives, design, implementation work and to assess the post-construction lifetime phase, which is most relevant for SWBE structures. From a wider point of view, when looking at the multitaxonomic diversity in both terrestrial and aquatic habitats, it has been shown that SWBE techniques could enhance global riparian habitat quality by allowing a greater richness and density of pioneer tree species. The use of phytosociology has become more important for the application of SWBE structures as nature-based vegetation composition. Specific challenges arise for river managers and practitioners with invasive alien species and climate change forcing us to redefine what is meant by ‘non-native’ species. Therefore, using a local and historical phytosociological typology to define the reference to be achieved could become increasingly misleading. By analyzing the ecological value of SWBE structures, another aspect must be considered from an ecological point of view. The possible negative impacts on ecosystems caused by SWBE measures, during the period of construction (e.g., emissions, energy consumption, intervention in nature) should be taken into consideration. A popular methodology to provide the possibility of achieving a better understanding of environmental burdens and to assess the potential environmental impact of products or services is environmental life cycle assessment (LCA). We are faced with the problems of climate change which means that we have to optimize our civil engineering (including SWBE) construction activities in terms of positive effects, for example urban heat islands or carbon storage and also any potential negative effects, for example emission of greenhouse gases or energy demand.We must critically examine our model of the SWBE approach, the application of SWBE techniques does not automatically mean an ecological improvement. SWBE systems are dynamic and always different, depending on their field of application. A harmonization of strategies and goals needs to be developed in order to support coherent measures aimed at improving the ecological status of river bodies, coastal areas and at the same time, guaranteeing hydraulic safety and adequate protection of human activities from hydromorphological hazards (flooding, floodplain erosion, failure of river and coastal-related infrastructures).