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Mangrove–coral habitat is characterized by heterogeneity in the physical environment that allows it to be out of equilibrium with open ocean conditions, resulting in differentiation of local physical, chemical, and biological attributes. This chapter highlights how some mangrove habitats can act as alternate refuges for corals during climate threats, particularly increasing seawater temperature, high levels of solar radiation, and ocean acidification. Coastal ecosystems are interconnected and so any change in one coastal ecosystem will have an impact on other ecosystems. Similarly, recovery and resilience of coastal ecosystems like coral reefs depend on the degree of connectivity and support from the neighboring coastal ecosystems such as seagrass beds. Therefore, healthy seagrass beds are especially vital for the resilience of coral reefs, as they support the coral communities to adapt to climate change impacts. Corals compete with seaweeds for space on the reef. When corals are healthy, the coral–seaweed competition reaches a balance. But, if the corals are not able to do well because of smothering like eutrophication or climate change induced impacts, then seaweeds can take over. Our study results suggest that coral reefs may become increasingly susceptible to seaweed proliferation under ocean acidification. Though the functional links of mangroves, seagrasses, and coral reefs have been studied, their conservation and management aspects due to connectivity and their importance for humans is yet to be understood. Importance of interconnectivity in biodiversity richness is illustrated by presenting the bioresource availability in the existing heterogeneous coral reef, seagrass, and mangrove habitats of the Neil Island, the Andamans and studies on the interactions among them are essential for conservation and management of such precious ecosystems.