Water projects designed to extract fresh water for local urban, industrial and agricultural use throughout rivers and estuaries worldwide have contributed to the fragmentation and degradation of suitable habitat for native fishes. The number of water diversions located throughout the Sacramento-San Joaquin watershed in California's Central Valley exceeds 3300, and the majority of these are unscreened. Many anadromous fish species are susceptible to entrainment into these diversions, potentially impacting population numbers. In the laboratory, juvenile green sturgeon (Acipenser medirostris) have been shown to have high entrainment rates into unscreened diversions compared with those of other native California fish species, which may act as a significant source of mortality for this already-threatened species. Therefore, we tested the efficacy of a sensory deterrent (strobe light) and two structural pipe modifications (terminal pipe plate and upturned pipe configuration) in decreasing the entrainment of juvenile green sturgeon (mean mass +/- SEM = 162.9 +/- 4.0 g; mean fork length = 39.4 +/- 0.3 cm) in a large (>500 kl) outdoor flume fitted with a water-diversion pipe 0.46 m in diameter. While the presence of the strobe light did not affect fish entrainment rates, the terminal pipe plate and upturned pipe modifications significantly decreased the proportion of fish entrained out of the total number tested relative to control conditions (0.13 +/- 0.02 and 0.03 +/- 0.02 vs. 0.44 +/- 0.04, respectively). These data suggest that sensory deterrents using visual stimuli are not an effective means to reduce diversion pipe interactions for green sturgeon, but that structural alterations to diversions can successfully reduce entrainment for this species. Our results are informative for the development of effective management strategies to mitigate the impacts of water diversions on sturgeon populations and suggest that effective restoration strategies that balance agricultural needs with conservation programmes are possible.