Tropical seascapes rely on the feedback relationships among mangrove forests, seagrass meadows, and coral reefs, as they mutually facilitate and enhance each other's functionality. Biogeochemical fluxes link tropical coastal habitats by exchanging material flows and energy through various natural processes that determine the conditions for life and ecosystem functioning. However, little is known about the seascape-scale implications of anthropogenic disruptions to these linkages. Despite the limited number of integrated empirical studies available (with only 11 out of 81 selected studies focusing on the integrated dynamics of mangroves, seagrasses, and corals), this review emphasizes the importance of biogeochemical fluxes for ecosystem connectivity in tropical seascapes. It identifies four anthropogenic drivers that can disturb these fluxes, including nutrient pollution, pH imbalance, disease outbreaks, and other forms of environmental degradation. This review also highlights significant knowledge gaps in our understanding of biogeochemical fluxes and ecosystem responses to perturbations in tropical seascapes. Addressing these knowledge gaps is crucial for developing practical strategies to conserve and manage connected seascapes effectively. Integrated research is needed to shed light on the complex interactions and feedback mechanisms within these ecosystems, providing valuable insights for conservation and management practices.