Ocean currents from the north generate a sandspit that pushes the mouth progressively southwards; however, the lower part of the estuary is periodically lost when the channel naturally realigns, or opens more directly to the sea at the north end before progressively again migrating south.
Floodgates restrict tidal action and flushing and diminish ecological values in the lower estuary by limiting the potential for long-term estuarine communities to establish. Higher up the estuary, conditions are much more stable, supporting saltmarsh and tidal flats with small freshwater lakes around the margins.
The Waikanae is usually freshwater dominated at low tide and at high tide consists of a freshwater layer on top of a saltwater layer. Plant and animal life is restricted to those that tolerate salinity extremes.
It is also one of very few sizable estuary and wetland areas in the southwestern North Island, and is a nationally significant wetland habitat for waders, seabirds and waterfowl, both local and migratory. More birds visit Waikanae Estuary Scientific Reserve than any other area in the Wellington Region.
The estuary is a local focal point for conservation, walking, picnicking, boating, fishing, paddling, bird watching, bathing, and whitebaiting. The system receives moderate inputs of nutrients and sediment from the catchment and treated wastewater enters the estuary from the Paraparaumu Treatment Plant via the Mazengarb Drain.
