Estuarine ecosystems are threatened by several human-induced pressures such as increased loads of sediments and nutrients from riverine sources, which has dramatically diminished the ecological health and condition of these ecosystems. In this study, we integrated rapid habitat mapping, traditional macrobenthic metrics (e.g., abundance, richness, diversity), and functional metrics (e.g., Rao quadratic entropy, functional richness, functional redundancy) to provide a holistic assessment of the ecological health of a cultural and economic valued estuary in New Zealand. Our integrative approach identified 11 different habitat classes across Waihī estuary and revealed that both traditional and functional metrics were different across the estuary. Our analyses also showed different benthic communities and functional traits across the sampling sites which were mainly driven by sedimentary conditions, in particular strong relationships with organic matter and mud content in sediment. More importantly, we showcased degraded ecological condition in several areas of the estuary, which overlapped with areas showing high concentrations of decaying algae, anoxic conditions, and low values of traditional and functional metrics. Our holistic approach, integrating mapping, traditional and functional assessments, showed to be a powerful tool for conservation and management, which could assist identifying ecosystem health and restoration actions.