Physical habitat losses for Pacific salmonids in California’s Central Valley motivate stream restoration. Considerable river morphodynamics affect the sustainability of habitat enhancing interventions. In addition, the presence of large dams in many river catchments causes low sediment supply. This study revises existing stream restoration techniques for their ecologically efficient and physically stable embedding in a 36-km testbed river. Ecological efficiency is evaluated in terms of a commonly used hydraulic habitat suitability index. Physical stability results from 2D hydrodynamic modelling of bed shear stress during steady flows of different flood frequencies. We differentiate between terraforming, stabilizing and maintaining stream restoration techniques, which constitute three feature layers. The first layer, terraforming, includes artificial terrain modifications such as grading or backwater creation to generate new habitat. These features require stabilization, which is provided by the second feature layer. The stabilization (layer two) is achieved by bioengineering such as placement of streamwood, angular boulders and vegetation plantings. The third feature layer has the purpose to maintain newly created habitat, e.g., through artificial gravel injections. We illustrate the application of the three-layer-approach at one major restoration site of the lower Yuba River using a self-written Python package. Ecohydraulic 2D modeling was applied to designs with incremental layer additions to evaluate newly created spawning habitat and feature sustainability. This procedure represents a pertinent way for stream restoration planning, which avoids non-sustainable habitat enhancement features and implements ecologically as well as physically sustainable features only.