While dominated by intertidal sand and mudflats, the well flushed and often steeply incised estuary channels are deep and, particularly near the entrances, support a variety of cobble, gravel, sand, and biogenic (oyster, tubeworm) habitats. Salt marsh is a significant feature of the estuary (~10% of the intertidal), although has been greatly reduced from its historic extent, primarily through drainage and reclamation. Intertidal seagrass beds are sparse (~2%) and located almost exclusively near the well-flushed entrance channel and central basin of the eastern arm.
Overall, despite extensive historical habitat modification, significantly reduced habitat diversity, and large areas of mud-dominated sediments, Waimea Inlet retains many areas of very significant ecological value. However, the prevalence of mud-dominated substrate, the persistence of localised dense macroalgal beds, and pressures on salt marsh near the estuary margin from drainage and reclamation are key broad scale habitat stressors that threaten these values. Reductions in sediment loads, targeted management of localised nutrient inputs, and facilitating landward migration of salt marsh in response to sea level rise will be required to improve estuary condition.
Estuary sediments are co-monitored by Nelson City Council (1 site) and Tasman District Council (4 sites).
