Freshwater ecosystems and the fisheries they support are increasingly threatened by human activities. To aid in their management and protection, we outline nine key principles for supporting healthy and productive ecosystems based on the best available science, including laws of physics and chemistry apply to ecology; population dynamics are regulated by reproduction, mortality, and growth; habitat quantity and quality are prerequisites of fish productivity; connectivity among habitats is essential for movements of fishes and their resources; freshwater species and their habitats are tightly linked to surrounding watersheds; biodiversity can enhance ecosystem resiliency and productivity; global processes affect local populations; anthropogenic stressors have cumulative effects; and evolutionary processes can be important. Based on these principles, we provide general recommendations for managing and protecting freshwater ecosystems and the fisheries they support, with examples of successful implementation for each strategy. Key management strategies include engage and consult with stakeholders; ensure that agencies have sufficient capacity, legislation, and authority to implement policies and management plans; define metrics by which fisheries resources and management success or failure will be measured; identify and account for threats to ecosystem productivity; adopt the precautionary approach to management; embrace adaptive management; implement ecosystem-based management; account for all ecosystem services provided by aquatic ecosystems; protect and restore habitat as the foundation for fisheries; and protect biodiversity. Ecosystems are complex with many intertwined components and ignoring linkages and processes significantly reduces the probability of management success. These principles must be considered when identifying management options and developing policies aiming to protect productive freshwater ecosystems and sustainable fisheries.