Sustainable concepts of ecologically functional rivers challenge engineers, researchers, and planners. Advanced numerical modeling techniques produce nowadays high-precision terrain maps and spatially explicit hydrodynamic data that aid river design. Because of their complexity, however, ecomorphological processes can only be reproduced to a limited extent in numerical models. Intelligent post-processing of hydrodynamic numerical model results still enables ecological river engineering measures to be designed sustainably. We have embedded state-of-the-art concepts in novel algorithms to effectively plan self-maintaining habitat-enhancing design features, such as vegetation plantings or the artificial introduction of streamwood, with high physical stability. The algorithms apply a previously developed lifespan mapping technique and habitat suitability analysis to terraforming and bioengineering river design features. The results not only include analytical synopses, but also provide actively created, automatically generated project plans, which are optimized as a function of an efficiency metric that describes “costs per m² net gain in seasonal habitat area for target species”. To make the benefits of these novel algorithms available to a wide audience, we have implemented the codes in an open-source program called River Architect. In this contribution, we present the novel design concepts and algorithms as well as a case study of their application to a river restoration project on the Yuba River in California (USA). With River Architect, we ultimately created an objective, parameter-based, and automated framework for the design of vegetative river engineering features. In addition, we are able to define a framework for stable and ecologically viable terraforming features, but part of the planning of earthworks is still left to expert assessment. Thus, improving the algorithms to plan terraforming of permanent, self-sustaining, and eco-morphodynamic riverbed structures based on site-specific parameters is one of the future challenges.