Résumé
Tropical estuaries are hyper‐diverse ecosystems, hosting essential habitats for freshwater, euryhaline, and marine life. Understanding how biological communities are distributed in these systems has long been a challenge because of their inherent dynamic nature and the diversity of interacting natural pressures and anthropogenic stressors they are subjected to. In addition, most studies focus on a single taxonomic group, hindering a comprehensive understanding of the interactive effects of natural and human‐driven environmental variations on the different components of tropical estuarian biodiversity. In this study, we used environmental DNA (eDNA) metabarcoding to examine the structure of multi‐taxonomic communities, from diatoms to fish, and their relationships with environmental drivers in three differentially impacted locations facing the Great Barrier Reef in Central Queensland (Australia). We first demonstrated that eDNA signals from sediment and water matrices provide complementary information and that both should be monitored for a more holistic understanding of community trajectories in anthropogenically impacted aquatic environments. We also observed that, independently of the taxonomic group considered, communities were primarily structured by the ecological conditions of the estuary. A within‐estuary differentiation along an upstream–downstream gradient was detected but only for small‐bodied organisms, which further adds credence to eDNA approaches as an ecologically relevant tool for monitoring fine‐scale biodiversity patterns even in profoundly dynamic environments. Finally, the different communities exhibited contrasting response patterns, in terms of diversity, composition, and uniqueness, to the anthropogenic gradient. Hence, our findings emphasize the need for multi‐taxonomic assessments, for which eDNA is well suited, to better understand the impacts of multiple stressors on biodiversity and thereby assist decision makers in the protection and management of tropical estuaries.