Monitoring estuary health

​​What we are doing

Environment Southland has been monitoring six estuaries, two harbours and one lagoon as part of its estuary programme.

In 2000, monitoring started on the four largest estuaries on the south coast; Waikawa Harbour, New River, Jacobs River and Toetoes Estuaries. Haldane Estuary and Bluff Harbour were added by 2005, and in 2008 monitoring began in Waimatuku Estuary, Waiau Lagoon and Freshwater Estuary on Stewart Island. Freshwater Estuary is monitored as a 'control' or unmodified estuary, to compare other estuaries to.

Environment Southland follows the Estuary Monitoring Protocol which has four parts; broad scale habitat mapping, fine scale sediment analysis, algal bloom mapping and vulnerability/risk assessments. We measure the indicators below to give an indication of the overall health of the system, and ranging from 'very good' to 'poor'.

What we measureIndicators​
Soft mud
  • Muddiness
  • Area of soft mud
  • Sedimentation build-up​
Habitat quality​
  • Extent of seagrass beds
  • Estuary invertebrates​
Nutrient enrichment​
  • Macroalgae cover
  • Sediment oxygen levels
  • Sediment nutrient concentrations

Soft mud​

Soft mud.PNG



Oxygenation Layer (ha or % area)​

oxygenation layer.PNG

Macroalgae cover/condition (Ecological Quality Rating)​

macroalgae cover.PNG

Sea Grass loss (% area change from baseline)

sea grass loss.PNG

Gross Eutrophic Zone (GEZ) (ha or % area)

A "Gross Eutrophic Zone" is defined as an area that has low sediment oxygenation (<1cm aRPD), soft mud (>25% mud content) and the presence of high macroalgal cover (>50% cover), these areas are in poor condition and can no longer support most estuarine animals and shellfish.

gross eutrophic zone.PNG

Estuary types

Estuaries are so much more than sand, mud and water. Like the organs in our bodies, different parts of the estuary have different functions. As the saying goes: the whole is greater than the sum of its parts.

Estuaries are naturally productive environments due to the input of nutrients from the land. However, there's a fine balance between having enough nutrients for a healthy ecosystem and too much. This can lead to a reduction in estuary health and function.

Even though we categorise estuaries into groups, no two estuaries are exactly the same. Some estuaries are more sensitive than others.

Sensitivity is related to factors such as:

  • Catchment nutrient load
  • Nutrient accumulation
  • Estuary size, shape and depth
  • River flow and volume
  • Tidal influence

Estuaries can be categorised in many different ways. We've grouped Southland's estuaries into three broad categories according to their risk of eutrophication. Eutrophication is when a water body becomes (too) enriched with nutrients causing the dense growth of plant life (phytoplankton, macroalgae, macrophytes). Excess plant growth changes estuarine habitats so they are no longer suitable for many species to survive.

Susceptibility to eutrophication is linked to a range of factors including: nutrient load, depth, water residence time, inflow volume, estuary volume and intertidal areas.

There are also geomorphological, energy and biogeographical factors that influence susceptibility to eutrophication. These include: current speed, volume and circulation patterns.

Very sensitive – High eutrophication risk

Estuaries with the greatest risk of eutrophication are enclosed lagoons that are usually closed to the sea, but occasionally open. They are typically shallow lagoons, fed by streams with relatively low water flow and volume.

When closed to the sea, these estuaries effectively act like a catchment lake. In developed catchments, contaminant load from inflowing streams can accumulate to high levels. Contaminant levels only reduce when the lagoon is open to the sea.

Southland examples: Waituna Lagoon, Lake Brunton, Waiau Lagoon, Waimatuku Estuary

Moderately sensitive – Moderate eutrophication risk

Estuaries with moderate risk of eutrophication are typically shallow, fed by rivers of moderate water flow and volume, have large intertidal areas of sand or mud, and are moderately influenced by tidal flow.

In developed catchments, contaminant load from inflowing streams and rivers can accumulate to high levels in upper estuary tidal flats. Lower reaches of the estuary are more affected by tidal currents and less prone to contaminant build up.

Southland examples: Haldane, Waikawa, New River, Jacobs River and Freshwater estuaries

Less sensitive – Low eutrophication risk

Estuaries with the lowest eutrophication risk are high 'energy' systems that are fed by high flow, high volume rivers. They have smaller intertidal areas than others due to the greater volumes of water flowing through them from riverine sources.

In developed catchments, contaminants found in river water are quickly transported out to sea, spending less time in the estuarine area.

Southland example: Toetoes (Fortrose) estuary

Did you know? Seawater doesn't simply flow in and out of an estuary en masse with the tide. The speed and direction of tidal currents at the estuary entrance are affected by the narrowness and depth of the estuary 'mouth'. Water flow is also affected by sandbanks, rocky outcrops, shoreline contours, structures and reefs.

Page reviewed: 05 Mar 2019 12:36pm