Many western U.S. landscapes are managed for multiple objectives, including biological conservation, commodity production, human welfare, and recreation. Effective conservation of special-status species in managed landscapes is challenging when species protection must be balanced with broader land-management objectives. In managed river systems, actions such as channel maintenance, bank stabilization, dam operation, and habitat enhancement are often implemented to achieve objectives related to water delivery, flood control, protection of adjacent lands, public recreation, and biological conservation. However, these actions are often constrained by the presence of special-status species because of regulatory requirements that may supersede implementation of other measures. Strategies to balance special-status species conservation with broader management objectives are directly informed by robust data sets on species abundance and distribution. On lower Cache Creek in Yolo County, California, multi-objective management seeks to balance protection of the federally-threatened Valley elderberry longhorn beetle (Desmocerus californicus dimorphus) and its sole host shrub, blue elderberry (Sambucus nigra ssp. caerulea), with channel maintenance, bank stabilization, and habitat enhancement actions. We conducted a comprehensive field survey from 2015 to 2016 to map all elderberry shrubs across the 904-ha Cache Creek Resource Management Plan area. An estimated 10,296 shrubs that spanned small, medium, and large size classes were mapped, strongly suggesting that the local population has been increasing since in-channel mining ceased in 1996. Analyses of shrub distribution relative to floodplain inundation zones, and associated vegetation, slope, and aspect revealed that most shrubs occurred in association with other woody riparian vegetation and within the ≤ 10-yr floodplain inundation zone. In addition, shrubs occurred more often than expected on intermediate slopes and both westerly and northwesterly aspects. The results of this study are guiding adaptive management and informing project planning and permitting on lower Cache Creek, demonstrating the importance of spatially-explicit abundance and distribution data for special-status species in managed landscapes.