The mangrove-seagrass-coral reef continuum is of immense ecological and socio-economic importance, supporting biodiversity, carbon storage, coastal protection, fisheries, and tourism. The presence of extreme environmental conditions along this continuum could support adaptive refugia for climate-sensitive taxa such as reef-building corals but physicochemical conditions are rarely assessed at sufficient spatiotemporal resolution. Furthermore, coastal development and low water quality increasingly threaten these interconnected coastal ecosystems. Yet, time-integrated pollution monitoring is absent at most locations. Here, we used a multi-disciplinary approach to assess benthic cover, coral diversity, and >20 abiotic parameters characterizing two mangrove- and seagrass-dominated inland bays and two nearby coral reefs in Curaçao (southern Caribbean) during the cool, dry season and warm, wet season. This was combined with time-integrated pollution monitoring using bioindicators to assess nutrients and trace metal pollution (inland bays only), and passive samplers and bioassays to assess organic chemical pollution (all four sites) during the wet season. This approach revealed a previously undocumented extent of strong diel and seasonal environmental variability in the two inland bays, with temperature, pH and dissolved oxygen frequently reaching values predicted under moderate-to-severe future climate scenarios. In addition, the inland bays had greater nutrient concentrations (especially ammonium) and ecotoxicological risks than the nearby reefs during the wet season due to run-off, industrial- and wastewater effluents, ports and boating. Overall, our findings show that Curaçao’s inland bays have significant potential to serve as natural laboratories to study the effects of future ocean conditions on resident taxa in situ. This however applies within the context of strong diel fluctuations and with the caveat of co-occurring stressors. Our work confirms the important role of mangrove and seagrass habitats as resilience hotspots for climate-sensitive taxa but also highlights the urgent need to improve monitoring, water quality and protection of these valuable habitats along the mangrove-seagrass-coral reef continuum.