Biodiversity is crucial for maintaining ecosystem stability and functionality under increasing anthropogenic stress. Part of this resilience comes from having many species performing the same function (functional redundancy) leading to the quantification of community composition and functional redundancy in relation to increasing stress. However, much of the research within coastal ecosystems focuses on distinct areas, rather than whole ecosystems. Here, we investigate the relationship between biodiversity and functional redundancy across two environmental gradients (sediment mud content and water column depth) and different habitat types following a survey of benthic macrofauna and sediment characteristics at 24 sites within Whangārei Harbour, New Zealand. We observed strong gradients in biodiversity which fragmented communities into fewer species that were a subset of the wider community. The lowest biodiversity was observed at muddy, intertidal and shallow subtidal sites which also had the lowest predicted functional redundancy. We show the stronger influence of water column depth on predicted functional redundancy than sediment mud content, highlighting the importance of subtidal regions. Overall, our study highlights the importance of studying the individual contributions of different areas in a landscape to characterise effective colonist pool size and how this can be used to predict recovery potential following disturbance.