Eutrophication.  High nutrient levels can cause 'blooms' of phytoplankton and algae. This can significantly alter predator/prey relationships in an area; it can reduce light levels (affecting species like seagrass and the fish that rely on this habitat); and can also lead to eutrophication of the seabed. Particularly, this affects habitats in sheltered waters and can potentially affect fisheries that rely on habitats in these places for some part of their life cycle.

Current information suggests this is overall a minor risk to fisheries. However, it could pose a significant risk in enclosed waters (eg harbours and estuaries) that have important nursery habitats.

Nutrient runoff - mostly from intensive farming - is thought to be raising nutrient levels in many harbour and estuarine areas. However, there has been very little research or monitoring of this issue.

In parts of New Zealand where farming has intensified over the last decade or two, nutrient levels in some enclosed inshore waters will likely rise significantly (as waters high in dissolved nitrogen slowly make their way through groundwater tables).