Levees are recognized as disconnecting rivers from their floodplains resulting in disruption of important functions, including fluxes of water and nutrients, and causing reduced hydrologic and habitat heterogeneity, biodiversity, and abundance. The flood protection provided by levees is also often threatened by increased high flows resulting from climate change. But in many landscapes levees are still necessary and so there is a need to better understand how levees can be redesigned to minimize negative effects. The levees along the lower Pajaro River in central California are being set-back to provide increased flood protection, but this project may also yield ecological benefits by expanding floodplain between the levees. To determine what ecological benefits might be obtained, we examined how levees affect temperature refugia, denitrification, ecological health, and biodiversity by comparing sections of the river with and without levees. Less denitrification (estimated by differences in mass-balance, N and O isotopes, and mRNA expression) was observed in sections with levees. The prevalence of temperature refugia (areas with summer temperatures less than 20°C in a thermal-drone survey) was greater in sections without levees. We used the California Stream Condition Index (calculated from macroinvertebrate samples from four sites with levees and one without) as a proxy for ecological health. Index scores were low for all sites indicating very likely alteration due to agricultural runoff containing excess nutrients, pesticides, and fine sediments regardless of the presence or absence of levees. Biodiversity is being assessed using an eDNA metabarcoding approach. Once the levees have been moved back, we will remeasure these same end-points to determine the changes in ecological condition achieved by the project. These results will inform managers of the potential for increasing ecological resilience in leveed rivers while improving flood protection.