Human-induced habitat clearing and pollution are leading drivers of biodiversity loss. Ecosystem assessments are required to identify ecosystems at risk of collapse, but they should account for cross-system linkages and dynamics where necessary. This is particularly true for coastal wetlands (e.g. seagrass, mangroves and saltmarsh), which exhibit high ecological connectivity and have individually suffered global declines over the last century. We use the coastal wetlands of Moreton Bay, Queensland, Australia, as a model system to examine how integrating outcomes of multiple, simultaneously conducted, ecosystem assessments can assist in identifying appropriate management and conservation strategies. We simultaneously conducted separate assessments of seagrass, mangrove and saltmarsh ecosystems against the IUCN Red List of Ecosystems criteria. Despite substantial human population growth in the region, seagrass and mangroves were assessed as Least Concern. Mangroves were found to be rapidly encroaching on saltmarsh. This process, together with past clearing, were the major drivers behind saltmarsh being assessed as Endangered. Given the importance of connectivity among these connected ecosystems, collapse in any one ecosystem can have seascape-wide consequences, highlighting the benefit of conducting multi-ecosystem assessments. Consequently, a fully integrated assessment of the coastal wetlands as a single entity would miss key processes, such as mangrove encroachment, potentially underestimating overall risks. Our study highlights the plight of saltmarsh and the value of conducting simultaneous RLE assessments for multiple ecosystems comprising seascapes. We recommend that connectivity be accounted for explicitly in assessments of other connected, high-risk ecosystems.