Monitored Estuaries

Estuaries are semi-enclosed coastal bodies of water where freshwater from rivers and streams flows into and mixes with saltwater from the ocean. Estuaries are very dynamic ecosystems and undergo rapid changes in water chemistry, such as shifts in water temperature, salinity and turbidity. Factors influencing these shifts include the tide, freshwater inflows, wind and the shape of the estuary.

A wide range of habitats are found within estuaries; from sub-tidal reefs, inter-tidal mud flats, mangrove and sea grass beds to landward margin vegetation, including herb fields, rush-land and sedge-land. These habitats support a diverse range of life; birds, shellfish, fish, and invertebrates, with many species using estuaries for part, or all of their life cycle.

People value estuaries for harvesting food, recreation, bird watching and for their biodiversity values. As the population increases our coastal areas come under pressure and estuaries often suffer from human activities such as run-off from agriculture and wastewater discharges increasing sediment and nutrients. Sedimentation, excessive nutrients, toxic contaminants, disease risk and habitat loss are all major issues currently facing estuaries throughout Southland and New Zealand. Severely degraded estuaries can no longer support a wide range of habitats and species often die and are required to move to favourable areas.

Estuarine Reports

For a list of reports on estuaries currently monitored by Environment Southland click here.

Environment Southland's Estuary Monitoring Programme (ESEMP)

Environment Southland monitors eight estuaries, one harbour and one lagoon as part of its estuary programme. Estuaries are selected because of their biological and recreational values combined with being 'at risk' to degradation. In 2000, monitoring started on the four largest estuaries on the south coast; New River; Jacobs River; Waikawa Estuaries and Toetoes Harbour. Haldane Estuary and Bluff Harbour were added by 2005, and in 2008 monitoring began on Waiau Lagoon, Waimatuku 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:

Broad Scale Habitat Mapping:

A combination of aerial photography, detailed ground-truthing (info gathered in the field) and GIS-based digital mapping are used to record the primary habitat features present.

Fine Scale (detailed) Sediment Analysis:

Representative sampling sites are selected and samples are collected and analysed for physical, chemical and biological variables.

Physical and chemical analyses –

  • Particle size distribution (% mud, sand, gravel)
  • Nutrients and organic content
  • Trace metal contaminants
  • Salinity of the overlying water measured at low tide
  • Colour and texture described and average redox potential discontinuity (RPD) depth recorded (This is the level in the sediment which is no longer oxidising and in a healthy state)
  • Observations/photographs of general site appearance


  • Epifauna (surface dwelling animals) and infauna (animals within sediments) numbers and species composition are counted and described

Algal Mapping:

Macroalgae is an important feature of estuaries, contributing to its high productivity and biodiversity. However, when water receives too many nutrients combined with conditions, such as calm weather, nuisance blooms of rapidly growing algae can occur. Therefore, we map of the percent cover of macroalgae to determine its nuisance status.

Vulnerability/Risk assessments:

The Ecological Vulnerability Assessment (UNESCO 2000) is a tool used to represent how an estuary ecosystem is likely to react to the effects of potential “stressors” (the causes of estuary problems). The approach uses assessment techniques to produce a ‘vulnerability’ rating showing how potential stressors may affect the uses and values of an area.

Other Monitoring:

  • Condition Ratings - In order to help interpret monitoring results and assist how estuaries are managed, condition ratings are used. Condition ratings are used for both individual parameters, for instance macroalgal conditions or individual nutrient conditions, and to give an overall picture of estuary condition
  • Water Quality in some of the rivers/streams flowing into estuaries is monitored
  • Sedimentation rates in selected estuaries

Estuary Characteristics Table

  NRE JRE Toetoes Waikawa Haldane Freshwater Waiau Waimatuku Bluff/Awarua Bay
Size(ha) 4100 725 500 760 206 812 101 20  
Catchment area (km2) 3947.9 1570 5616 200 73.8 320 8260 150 118
Depth (m) 1.51 2.19 2.5 1.53 1.24 1.5 2.43 1.5 2.24
Mean River inflow (cumsec) 63.1 28.1 99.5 5 0.78 7.9 156 6.13 0.78
Dominant landuse exotic grass exotic grass exotic
native forest native
manuka /

Note - This table is populated from the Wriggle reports and the NIWA website coastal explorer and our own flow data generated from the Hilltop software and the hydrology department. Pink cells denote where there is not enough accurate data to estimate. Environment Southland is the brand name of Southland Regional Council.
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