Developing a resilient flood system will require decision making that does not just manage the surface water, but rather the dynamic interchange of surface water and groundwater horizontally across floodplains and vertically through the subsurface. Floodplain restoration through levee setbacks and topographic modification can be optimized to promote recharge while simultaneously sustaining ecosystem function. In this pilot study led by the DWR Flood-MAR program, a systematic approach is applied to identify floodplain enhancement opportunities and collaboratively design restoration projects that provide high-quality salmonid habitat and enhance naturally occurring floodplain recharge. The Ecological Floodplain Inundation Potential (EcoFIP) toolkit facilitates multiple levels of floodplain reconnection opportunities identification, analysis, and prioritization. New workflows were developed for the pilot study to visualize and compare conceptual restoration designs for potential habitat and recharge benefits against their respective implementation costs. The San Joaquin River pilot study demonstrated a scalable approach to align programmatic support needed to increase the pace and scale at which multi-benefit floodplain projects can be conceptualized, evaluated, and advanced towards implementation.