Flats ecosystems are dynamic, shallow, nearshore marine environments that are interconnected and provide immense ecological and socio-economic benefits. These habitats support a diversity of fish populations and various fisheries, yet they are increasingly threatened by anthropogenic stressors, including overfishing, habitat degradation, coastal development, and the cascading effects of climate change. Effective habitat management and restoration are essential but are often missing for flats ecosystems. Despite navigating a landscape of imperfect knowledge for these systems, decisive action and implementation of habitat protection and restoration is currently needed through policy and practice. We present a comprehensive set of 10 strategic guiding principles necessary for integrating habitat management and restoration for the conservation of interconnected flat ecosystems. These principles include calls for comprehensive ecosystem-based ­management, integrating adaptive strategies that leverage diverse partnerships, scientific research, legislative initiatives, and local and traditional ecological knowledge. Drawing on successes in other environmental management realms, we emphasize the importance of evidence-informed approaches to address the complexities and uncertainties of flats ecosystems. These guiding principles aim to advance flats habitat management and restoration, promoting ecological integrity and strengthening the socio-economic resilience of these important marine environments.