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Methods - how we monitor

Where and how we collect the data

Monitoring sites

Thus far, six estuaries have been monitored. Click to see a map where the seven estuaries are located. Each has been monitored for one year.  Four locations are usually sampled in each estuary.  For example, the map below shows the four sites sampled at the Kawhia estuary.  Site 1 is closest to one of the larger freshwater inflows, while site 4 is closest to the sea.  Sites 2 and 3 are intermediate.  The sampling sites in the other estuaries were distributed in a similar way.

Estuarine image 

Figure 1: Kawhia Harbour, on the west coast of the Waikato region, showing the four water quality sites that were sampled during 2008–09. Intertidal sandflats and mudflats are shown shaded. 

Monitoring frequency

A new estuary is monitored every second year.  During the 12-month period of monitoring, there are usually a total of eight visits.  Six of these are at 2-monthly intervals, while the remaining two occur after a periods of heavy rain. 

Data history

Waikato Regional Council began monitoring estuarine water quality in 1999.  Whangamata was monitored in 1999–2001; Raglan in 2002–03, Whangapoua in 2006–07, Southern Firth of Thames in 2006–07, Kawhia in 2008–09, Whitianga in 2010-11 and Port Waikato in 2012-13. 

Measurement technique

Sites are generally visited within an hour of mid-tide on an outgoing tide.  Water quality at individual sites changes during the tidal cycle, and mid-tide is regarded as a reasonable time for determining average conditions. At Port Waikato, however, the sampling was undertaken within an hour of high tide, because the relatively high flow of the Waikato River meant that at other stages of the tide the water present there was almost entirely fresh. Even so, seawater comprised less than three percent of the mix in about one-third of the high tide samples from Port Waikato.

Water quality is measured by making some measurements on site (for example, water temperature, salinity and dissolved oxygen) and by taking samples of water back to the laboratory for analysis.  A total of about 16 water quality variables are measured, including:

  •  physical variables (for example, temperature, turbidity)
  •  chemical variables (for example, salinity, dissolved oxygen, nitrogen, phosphorus)
  •  microbiological variables (for example, algal biomass, faecal coliform bacteria).

Quality control procedures

Quality control measures are undertaken in accordance with Waikato Regional Council’s ISO 9001:2000 standards including procedures for the collection, transport, storage of samples, and methods for data verification and quality assurance to ensure the consistency of data across the programme.  Samples are sent to IANZ registered laboratories for analysis.  Back-up samples are held for two months until results have been verified by routine quality assurance procedures.  

How this indicator is compiled

All data from field measurements and laboratory analyses are stored in Waikato Regional Council’s water quality archiving database.

The indicator has three parts:  (1) water quality for ecological health, (2) water quality for contact recreation, and (3) water quality for shellfish-gathering.  In each case, three categories of water quality were developed:  excellent, satisfactory and unsatisfactory.  These were based on the “critical values” for the relevant water quality variables.

We identified the following seven water quality variables as being relevant to the suitability of estuarine water quality for ecological health:

  1.  dissolved oxygen
  2.  pH
  3.  turbidity
  4.  total ammonia
  5.  nitrate
  6.  total phosphorus
  7.  chlorophyll a

We identified the following water quality variable as being relevant to the suitability of estuarine water quality for contact recreation:

  1.  enterococci – single sample

We identified the following water quality variables as being relevant to the suitability of estuarine water quality for shellfish-gathering:

  1.  faecal coliforms – median at individual sites
  2.  faecal coliforms – 90 percentile at individual sites

Check out the critical values for the three categories that were derived from national or other standards and guidelines, and from expert opinion. 

At each estuary, the proportion of all samples collected during each monitoring period (usually one year) for a given water quality variable which met the standard for excellent water quality was determined.  Similarly, the proportions which met the standards for satisfactory and unsatisfactory water quality were determined.  This process was undertaken for all ten variables. 

At each estuary, the average value of the proportions found to be “excellent” for each of the water quality variables was calculated.  Average proportions for the “satisfactory” and “unsatisfactory” categories were also calculated.  The results for the individual estuaries were then aggregated to provide a value for a “typical Waikato estuary”. 

Find out what percentage of samples in each estuary met our guidelines for water quality for ecological health, for contact recreation and for shellfish-gathering. 

Guidelines and standards

The table below lists the water quality guidelines and standards used.

Table 1: Guidelines and standards used to assess estuarine water quality for ecological health, for contact recreation and for shellfish-gathering.

Water quality variable (units) Relevance Categories
Excellent Satisfactory Unsatisfactory
Ecological health
Dissolved oxygen (% of saturation) Oxygen for aquatic animals to breathe >90 80 – 90 <80
pH Can affect plants and fish 7.5 – 8 7 – 7.5 or 8 – 8.5 <7 or >8.5
Turbidity (NTU) Can restrict plant growth <2 2 - 10 >10
Total ammonia (g N/m3) Toxic to fish <0.1 0.1 - 0.91 >0.91
Nitrate (g N/m3) Causes nuisance plant growth <0.005 0.005 – 0.015 >0.015
Total phosphorus (g/m3) Causes nuisance plant growth <0.01 0.01 – 0.03 >0.03
Chlorophyll a (g/m3) Algal blooms <0.002 0.002 – 0.004 >0.004
Contact recreation
Enterococci, single sample (no./100 mL) Human health <28 28 – 280 >280
Faecal coliforms, median (no./100 mL) Human health <2 2 – 14 >14
Faecal coliforms, 90 percentile (no./100 mL) Human health <6 6 - 43 >43

The guideline values for satisfactory water quality for contact recreation and for shellfish-gathering are from New Zealand’s “Microbiological water quality guidelines for marine and freshwater recreational areas” (Ministry for the Environment and Ministry of Health 2003). 

The guidelines for satisfactory water quality for ecological health are from the Australian and New Zealand Environment and Conservation Council’s “Australian and New Zealand guidelines for fresh and marine water quality” (2000).  Noting that no guidelines for New Zealand estuaries were available, ANZECC recommended that the guidelines for estuaries in south-east Australia be used instead.  This has been done here. 

In each case, expert judgement has been used to identify the guidelines for excellent water quality. 


  • The aggregation of water quality within a given estuary ignores any differences between the individual sites in that estuary.
  • Levels of faecal coliforms and enterococci are known to vary markedly with time, and particularly following periods of wet weather, so eight visits per estuary (six “dry” and two “wet”) probably provides only a broad indication of typical levels.
  • Because the samples are collected from the open water of the estuaries (using a boat), the results are less relevant to conditions along the shoreline where people may also wish to swim or to gather shellfish.  Localised inflows or seeps of contaminated freshwaters can mean that shoreline areas are less suitable for these activities.