The ability of the ocean to continue to sustain human society depends on adequate protections of its ecosystem function and services. Despite the establishment of marine protected areas, formal protection of critical connectivity corridors to link habitats and thereby maintain necessary demographic transitions in marine species under threat is now rare. Such protections are critical to future resilience of food webs as climate and ocean change continues. Here, we focus on the Gulf of Mexico to support an integrative, holistic approach to marine and coastal habitat restoration, rehabilitation, and conservation in an ecosystem context following the extensive environmental and living resource injuries from the Deepwater Horizon oil well blowout. Critically important physical, chemical, and biological connectivity processes drive nutrient transport from the nearshore, mid-waters, and even deep ocean into coastal terrestrial habitats, enhancing primary production and terrestrial species populations. The emerging scientific understanding of the nature, habitat specificity, locations, and directions of transport in connectivity processes can help build natural ecosystem capital through protecting flows from land to sea and from the sea to multiple coastal habitats. We expose a dire need for a new conservation imperative, recognizing that oceanic and coastal protected areas established around the reliance of individual species on critical habitats are insufficient without also conserving relevant connectivity corridors that service ontogenetic migration pathways and ecosystem-support processes. Such connectivity must be explicitly understood, protected, and often actively enhanced through restoration intervention to ensure the success of various site-specific conservation actions and be continually modified in anticipation of and in response to multiple impacts of changing climate.