Methods - how we monitor estuary health | Waikato Regional Council

Regional Estuary Monitoring Programme (REMP)

Monitored estuaries •
Where and how we collect the data

Monitored estuaries

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Firth of Thames
Whaingaroa (Raglan) Harbour
Tairua Harbour
Coromandel Harbour

Firth of Thames

The Firth of Thames is a large compound estuary and a drowned river valley. It has a catchment area of 4194 km² and is the primary receiving environment for the Hauraki Catchment. It is New Zealand’s largest shallow marine embayment. At its southern end several rivers (in particular the Waihou and Piako Rivers) drain into the estuary and at its northern end it opens into the Hauraki Gulf. The harbour is also used for a range of recreational activities, for commercial and recreational harvesting of seafood and aquaculture. The Firth of Thames is a site of cultural significance to Hauraki iwi.

The south-western shore of the Firth of Thames is recognised as an internationally important wetland under the Ramsar Convention (one of six sites within New Zealand). The Firth of Thames Ramsar site includes around 7,800 hectares of shallow estuarine waters, intertidal mudflats, mangrove and saltmarsh, and graded shell beach ridges. It is ranked as one of New Zealand’s three most important areas for shorebirds.

The Miranda Wildlife Refuge and nearby wetlands, which make up a significant portion of the Ramsar site, are a seasonal home to thousands of wading birds and shorebirds. From spring onwards, large numbers of migrant birds, particularly godwits and knots, begin arriving to feed. Many of these birds will have spent several weeks travelling south from breeding grounds as far away as Siberia and Alaska. In autumn these birds fly north again. The refuge is also an important site for local species, such as the pied oystercatcher, New Zealand dotterel, variable oystercatcher and black-backed gull.

The Firth of Thames is also an important habitat for a range of common inshore fish species, many of them of cultural, recreational and commercial value. These include snapper, kingfish, jack mackerel, red gurnard, sand flounder and yellowbelly flounder. The Firth is also a nursery area for juvenile snapper, spotted dogfish, and hammerhead shark.

The Firth of Thames is under increasing pressure from human activities, including marine farming and the input of terrigenous sediment and nutrients due to the intensification of farming and urban development within the surrounding catchment.

Whaingaroa (Raglan) Harbour

Whaingaroa (Raglan) Harbour is a tidal lagoon and drowned river valley, with intertidal sand and mudflats making up about 70 per cent of its area. The catchment area for the harbour is 523 km².

Whaingaroa (Raglan) Harbour is an important habitat for resident, rare and threatened, and international migratory bird species. The critically endangered Maui’s Dolphin has been recorded in the harbour, although it is not known how much this species uses this area. The harbour is also used for a range of recreational activities, for commercial and recreational harvesting of seafood and is a site of cultural significance for Tainui iwi.

The clearance of native vegetation over the last century in the Raglan catchment, combined with steep terrain and unstable rock, has led to significant sediment input into the harbour. The Whaingaroa Harbour Care group was formed to improve the quality of the water entering the harbour by replanting coastal and stream margins. They have planted more than 2 million native trees in the harbour catchment since 1995.

Whaingaroa (Raglan) Harbour is under increasing pressure from human activities both around the harbour margin and further into the surrounding catchment.

Tairua Harbour

Tairua Harbour is a tidal lagoon-type estuary located on the east coast of the Coromandel Peninsula. The main river entering the estuary is Tairua River. During high rainfall events flash flooding can occur 3-5 times per year. The Harbour has a total area of 6km², with intertidal sand and mudflats making up approximately 51% of its area. It is sheltered from the sea by the Pauanui sand spit and Paku Mountain. The catchment area for the harbour is 280 km².
Vegetated habitats occupy around 39 per cent of the entire area of Tairua Harbour. Seagrass beds make up more than half the total vegetation cover, dominating the intertidal flats throughout the middle reaches. Mangroves and saltmarsh are also found in the harbour.
Tairua Harbour is recognised as an Area of Significant Conservation Value in the Waikato Regional Coastal Plan. The harbour is a significant site to Hauraki Iwi, and is known to support important ecological communities including marine invertebrates, shellfish beds and a range of inshore fish species (snapper, sand and yellowbelly flounder, kahawai, trevally and parore).
Tairua Harbour also provides habitat for rare and threatened wading and coastal bird species (New Zealand dotterel, banded dotterel and reef heron), and important whitebait spawning habitat. The harbour has high recreational use and is used for commercial and recreational harvesting of seafood.
Tairua Harbour is under increasing pressure from human activities within the harbour (marinas, jetties), around the harbour margin (urbanisation) and further into the surrounding catchment (forestry, land modification/farming).

Coromandel Harbour

Coromandel Harbour is a large coastal embayment type estuary, located in the Hauraki Gulf on the west coast of the Coromandel Peninsula. The harbour is sheltered from the sea by peninsulas to the north and south, and islands to the west, the largest being Whanganui Island. The harbour has a total area of 25.4 km², is shallow and dominated by large intertidal sand and mudflats making up approximately 21% of its area. It has a relatively small catchment area of 60 km².
Coromandel Harbour has extensive seagrass beds, along with significant mangrove stands and saltmarsh habitats. The harbour has high recreational use and is used for commercial and recreational harvesting of seafood. Many oyster farms are located within the harbour (intertidal areas) and mussel farms near the harbour entrance.
The harbour is a significant site to Hauraki Iwi and is known to support important ecological communities including marine invertebrates, shellfish beds and a range of inshore fish species (including snapper, flounder, kahawai and trevally). Coromandel Harbour also provides habitat for rare and threatened wading and coastal bird species (including New Zealand dotterel, banded dotterel, bar-tailed godwit).
In the past Coromandel Harbour received a high amount of sediment and nutrients from mining and land clearance in the catchment. The harbour is currently under increasing pressure from human activities within the harbour (marinas, jetties, marine farming), around the harbour margin (urbanisation) and further into the surrounding catchment (forestry, land modification/farming). These activities in the catchment are contributing to high levels of sediment entering the harbour.

Where and how we collect the data

Sediment-dwelling organisms and sediment characteristics are monitored at five sites in the Firth of Thames, six sites in Whāingaroa (Raglan) Harbour, five sites in Tairua Harbour and four sites in Coromandel Harbour. Monitoring sites are distributed throughout the main part of each estuary and are located at the mid-intertidal level of sand and mud flats.

Monitoring is currently undertaken once per year in spring (i.e. between September and November). Monitoring began at the Firth of Thames and Whāingaroa Harbour in 2001, at Tairua Harbour in 2012, and Coromandel Harbour in 2019.
At each monitoring site ten sediment samples are collected using a 13 cm (diameter) by 15 cm (depth) sediment corer. Each plot is approximately 10,000 m2 (100 m x 100 m), and is divided into 10 equal-sized sectors. Within each sector a random location is selected and a core sample taken. Cores taken in adjacent sectors must be at least five metres apart.

Sediment-dwelling organisms are separated from the sediment using a 500µm mesh sieve. The sample is then preserved in 70 per cent isopropyl alcohol and treated with a dye (called Rose Bengal) that stains the animal tissue pink. Staining helps with the extraction of sediment-dwelling organisms (e.g. marine worms, crabs and shellfish) from the sample which is predominantly a mixture of pebbles, sand and shell debris.

Back in the laboratory we separate the stained animals from the sediment and other debris, identify and count the sediment-dwelling organisms to the lowest practicable taxonomic level (generally species or species group), and then store the samples in 50 per cent isopropyl alcohol. The remaining non-living material (shell material, pebbles and sand) is dried at 70°C for 48 hours and weighed to determine the dry weight of each sample. In all samples shell material dominates the non-living material (typically much more than 90 per cent) so we refer to this material as shell hash.
At each monitoring site on each sampling occasion, five bulked surface sediment samples (5cm diameter, 2cm deep core) are collected from random locations within a 100m by 100m monitoring plot. Five replicate surface sediment scrapes are also collected at each monitoring location for analysis of microalgal biomass . Each sample is stored frozen and then analysed for a number of chemical and physical properties. These properties are:

Sediment grain-size: Grain size analysis was carried out by wet sieving. Samples were sieved through a stack of sieves (at 2000 µm, 500 µm, 250 µm, 125 µm and 63 µm) and the fractions remaining on the sieves dried at 60°C for 48 hours. Results were reported as the per cent by weight of the total sample. Grain size data were grouped into the following grain size categories: mud (<63 μm), very fine sand (63-125 μm), fine sand (125-250 μm), medium sand (250-500 μm), coarse sand (500-2000 μm) and gravel (>2000 μm) following the Wentworth sediment classification.

Sediment organic carbon and nitrogen content: Another sub-sample from each bulked sediment sample was analysed for total organic carbon and total nitrogen content using an automated CHN analyser. Samples were dried and finely ground before analysis. Sediment for total organic carbon analysis was pre-treated with acid to remove carbonate material prior to analysis.

Sediment microalgal biomass: Chlorophyll a was extracted from freeze dried sediment by boiling in 95 per cent ethanol and the extract analysed using a spectrophotometer. Acidification was used to separate plant degradation products (phaeophytin) from chlorophyll a.
At each monitoring site (except Te Puru in the Firth of Thames) between two and six concrete plates (30 cm x 30 cm) have been buried at a known depth beneath the sediment surface. During each sampling event the depth of sediment over these plates is measured by inserting metal (knitting) needles into the sediment above the plates and measuring the length of needle immersed in the sediment. This provides an indication of sediment accumulation onto the sand or mudflats at the monitoring sites.

Long-term sediment accumulation rates are very variable and therefore require detailed statistical analysis to extract trends from natural variability. A recent report has analysed sediment accumulation rates and reviewed methods for the Firth of Thames and Whāingaroa (Raglan) Harbour.
Total Organic Carbon (TOC) is derived from decaying vegetation, bacterial growth, and metabolic activities of living organisms or chemicals. The amount of TOC in sediment is a function of the various sources reaching the sediment surface and the rates at which different types of organic carbon are degraded by microbial processes during burial.
Total nitrogen (TN) is the sum of nitrate-nitrogen (NO₃-N), nitrite-nitrogen (NO₂-N), ammonia-nitrogen (NH₃-N) and organically bonded nitrogen measured in estuarine sediments. High organic nitrogen levels are due to the decomposition of aquatic life and sewage runoff while inorganic levels are enhanced by erosion and residential and agricultural runoff (i.e. fertilisers).
Chlorophyll a is a green pigment found in plants. It absorbs sunlight and converts it to sugar during photosynthesis. Chlorophyll a concentrations are an indicator of phytoplankton abundance and biomass in coastal and estuarine waters. Chlorophyll a is commonly used as a measure of water quality. High levels often indicate poor water quality and low levels often suggest good conditions. However, elevated chlorophyll a concentrations are not necessarily a bad thing. It is the long-term persistence of elevated levels that is a problem.
Phaeophytin is a breakdown product of chlorophyll-a.
The median grain size of a sediment sample is the midpoint of the grain size distribution: Half of the sediment is coarser and half is finer than the median grain size.
Grain size refers to the diameter of individual grains of sediment. Marine sediment grains typically vary in size from a few micrometres (µm = 0.001 mm) to a few millimetres. The grain size scale commonly used to describe grains of certain diameters is the Wentworth scale. We use the six Wentworth size classes shown in the table below. They range from mud (particles <62.5µm) to gravel (particles >1 mm).

Wentworth size class Micrometers (µm)*

Mud <62.5

Very fine sand 62.5-130

Fine sand 130-250

Medium sand 250-500

Coarse sand 500-1000

Gravel >1000

Shell hash are pieces of broken shell that are mixed in the sediment. Because of the way we process our samples, REMP shell hash samples include some pebbles and sand. However, these components are small (typically much less than 10%) so we are confident that our shell hash measurements are adequate.

Wentworth size class	Micrometers (µm)*
Mud	<62.5
Very fine sand	62.5-130
Fine sand	130-250
Medium sand	250-500
Coarse sand	500-1000
Gravel	>1000