Salmon populations along the western coast of the United States have exhibited widespread decline, primarily due to habitat disturbances such as dam construction, rerouting of waterways, and pollution. To address these challenges, this research assesses survival and behavior of juvenile Chinook Salmon within the highly modified environments of the Sacramento and Klamath River Basins. Both river systems were significantly altered at the turn of the 19th century to meet the demands of agriculture and urban development. The first two chapters of this dissertation investigate crucial aspects of juvenile Chinook Salmon survival within the agricultural floodplains of the Sacramento River. The first chapter examines the impact of habitat complexity on juvenile fall-run Chinook Salmon rearing success. The second chapter shifts focus to explore how different rearing environments affect juvenile fall-run Chinook Salmon outmigration survival and subsequent adult returns. The third chapter explores survival trends for yearling spring-run Chinook released in the Upper Klamath River Basin to inform a reintroduction program following the largest dam removal in United States history. Collectively, this research identifies critical areas of high fish mortality and proposes additional conservation measures to address these threats. Findings from each chapter offer valuable insights for fisheries managers, illustrating the challenges of managing species with complex life cycles in highly modified aquatic habitats.