The Philippine archipelago lies at the centre of global marine shore fish biodiversity and supports extensive mangrove forests, coral reefs and seagrass meadows that sustain coastal livelihoods, food security and shoreline protection. These ecosystems are under mounting pressure from aquaculture conversion, siltation, destructive fishing, coastal development, land subsidence and increasingly intense tropical cyclones. This review synthesises peer-reviewed literature on (i) the ecological processes that govern mangrove, coral reef and seagrass dynamics in the Philippines, (ii) the drivers and consequences of coastal erosion and hazard exposure, and (iii) the effectiveness of habitat restoration approaches. Philippine mangrove cover has declined substantially over the past century, largely through conversion to brackishwater fishponds, and long-term survival of planted mangroves has often been low because of inappropriate species and site selection. Philippine coral reefs have lost about a third of their hard coral cover within a decade, while seagrass species richness declines sharply under siltation and aquaculture effluent. Healthy reefs and mangroves substantially attenuate wave energy, yet their protective role is undermined by degradation, subsidence and maladaptive hard engineering. Restoration has advanced from monospecific mangrove planting and coral gardening towards hydrology-based mangrove rehabilitation, larval enhancement of corals and seascape-scale planning. However, restoration remains constrained by scale, limited monitoring and weak institutional integration. We propose a research and management agenda that couples ecosystem process knowledge with nature-based coastal protection, long-term monitoring and governance reform.