Maintaining or restoring connectivity in aquatic systems can enhance migratory fish populations; maintain genetic diversity in small, isolated populations; allow Organisms to access complementary habitats to meet life-history needs; and facilitate recolonization after local extirpations. However, intentional fragmentation may be beneficial when it prevents the spread of nonnative species or exotic diseases, eliminates hybridization between hatchery and wild stocks, or stops individuals from becoming entrapped in sink environments. Strategies for fragmenting aquatic systems include maintaining existing natural barriers, taking advantage of existing anthropogenic features that impede movement, severing artificial connectivity created by human actions, and intentionally creating new barriers. Future challenges for managing fragmentation include maintaining hydrologic connectivity while blocking biological connectivity in water development projects; identifying approaches for maintaining incompatible taxa, such as sport fishes and small nongame species; and developing selective barriers that prevent the passage of unwanted species while allowing normal life-history movements of other species.