Moutere estuary is valued for its aesthetic appeal, its rich biodiversity, shellfish gathering, swimming, water-skiing, waste assimilation, fishing, boating, walking and scientific appeal. A small commercial port and marina are located at the northern entrance.
Elevated nutrients, sediment, disease-causing organisms and possibly toxicants entre the estuary from catchment run-off. A fish-processing, fishmeal and icecream factory discharge at Port Motueka. Other stressors include the presence of seawalls, causeways, culverts, stormwater. As is the case with all estuaries sea level rise will remove saltmarsh habitat and the invasion of pests and weeds is ever-present.