Sedimentation / smothering. Muds and silts washed down into the nearshore area can significantly alter the biodiversity and productivity of fisheries and ecosystems through both direct and indirect effects. 

Current information suggests this is a significant risk to the productivity or sustainability of a number of inshore shellfish, crustacean and finfish fisheries.

Direct effects can include:
• clogging the gills of shellfish (eg cockles, pipi, scallops) and other filter feeders;
• reducing settlement success and survival of spores, larvae and juvenile invertebrates (e.g. kelp, paua, kina); and
• making it harder for some fish to see their food.
Indirect effects may be far greater. These include the modification or loss of important fish nursery habitats like green-shell and horse mussel beds, sea-grass meadows, bryozoan and tubeworm mounds, sponge gardens, kelps/seaweeds. These are vital nursery grounds for snapper, tarakihi, trevally, john dory, garfish, blue cod, grey mullet and other species.

Where sedimentation rate have been measured, they often show a higher sedimention rate in the latter 20th century than was the case earlier. Some regional councils have begun monitoring sediment deposition in some harbours and estuaries. But this work has not been at a broad enough scale to show significant trends.