What ails our estuaries - problems and solutions

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Let’s start with a few words about solutions. Estuaries are at the bottom of the freshwater drainage network and, effectively, are a part of it. This means that every time we act to protect and enhance streams and rivers we are also benefiting the estuary at the downstream end. There are lots of such actions available to us. For instance, we can keep stock out of streams, protect riparian margins, plant steep slopes with trees to control landslips, apply fertiliser at recommended rates (this is not just farmers: city gardeners, take note), and restrain ourselves from tipping paint into stormwater drains. Some of these things are clearly within the ability of the individual to achieve, whereas others require a “higher level” of action. This is where various local, regional and national authorities and agencies come in, usually acting under the umbrella of the Resource Management Act.

Find out more about the Resource Management Act

When it comes to curing estuary ailments, there is not a lot you can actually do inside the estuary. Why is this? To continue the metaphor, it is because estuary illnesses are caused by what happens on the land, so this is where the cure must be applied. In a very real way, if you look after the land, the estuary will look after itself.

Decline of seagrasses

Seagrasses have diminished worldwide – and this includes within New Zealand – which is of some concern because it has been found that it is very difficult to restore seagrass beds once they have become degraded. Common causes of degradation, which are discussed in some detail in 'The role of sediment in keeping seagrass beds healthy', include unnaturally turbid water, high sedimentation rates, and gradual replacement of sandy habitats with muddy sediments. All of these are symptoms of disturbed catchments.

Read our Water & Atmosphere article 'The role of sediment in keeping seagrass beds healthy'

Mangrove spread

It was mentioned previously that New Zealand’s mangroves are unusual in a couple of respects. This turns out to be true when it comes to issues concerning mangroves as well: New Zealand is one of the few (perhaps only) places in the world where people are concerned about the spread of mangroves. 'Spreading mangroves: a New Zealand phenomenon or a global trend?' explains that in most parts of the world, areas of mangroves are diminishing and mangrove ecosystems are under threat. Furthermore, people are concerned about that and are trying to prevent the rot. In contrast, New Zealand’s mangroves are expanding, with consequent unwelcome effects including reduced boat access, spread of smelly mud, loss of water views, poorer fishing and shellfish gathering, and decreased property values. Many New Zealanders are concerned about these issues, and are taking steps to actively control mangrove spread. The difference in the perception of the value of mangroves must stem, at least in part, from the different ways mangroves are used. For instance, mangroves are widely used overseas for timber, food, shelter and protection, which is not so much the case here. There is also a perception that New Zealand’s mangroves do not play a significant role in the larger estuarine ecosystem.

Read our Water & Atmosphere article 'Spreading mangroves: a New Zealand phenomenon or a global trend?'

Mangrove spreading in New Zealand in recent times is widely attributed to accelerated silt runoff from developing and deforested catchments (see 'Fringing habitats in estuaries: the sediment–mangrove connection'), which reduces water depth and expands the areas that are suitable for mangroves to colonise. Recent experimental work has indicated that you can stimulate mangrove growth by fertilising them with nitrogen (see 'Nutrient enrichment in mangrove ecosystems: a growing concern'). This discovery implies that elevated nitrogen levels in the water – from agricultural runoff, for example – may be fertilising mangroves and thereby assisting them to spread. This occurs through faster growth, and increased production of reproductive propagules.

Read our Water & Atmosphere article 'Fringing habitats in estuaries: the sediment–mangrove connection'

Read our Water & Atmosphere article 'Nutrient enrichment in mangrove ecosystems: a growing concern'

A discussion intended to inform the mangrove-control debate is provided in 'For and against mangrove control', which includes an assessment of various management options. It’s not a straightforward issue: although mangroves are a natural part of the ecosystem, and it is in their nature to spread, there may be valid reasons for controlling them. For example, retaining and restoring the sandy habitats that are being consumed by mangroves might lead to an overall increase in estuary biodiversity, and human amenity undoubtedly would be improved in many cases. On the other hand, mangrove control would prevent the estuary from “ageing naturally”, although just what this means in estuaries that already have unnaturally high sediment inputs is open to debate.

Read our Water & Atmosphere article 'For and against mangrove control'

It is interesting to wonder why it is that mangroves are expanding here but retreating overseas. In both cases, change in landuse is the root cause, but with different results. Here, catchment development has resulted in increased soil erosion and consequent larger sediment inputs to estuaries, which stimulates mangrove spread. In contrast, in Micronesia, India, Pakistan and Brazil, for example, damming of rivers has resulted in reduced sediment load to the coast, which starves mangroves of sediment. In India, extreme siltation has changed the paths of freshwater inflows so that mangroves no longer receive sufficient tidal flushing, which causes them to decline.

Turbid water

As far as shellfish go, turbidity – or, more precisely, suspended particulate matter (SPM) in the water column – is both necessary and fatal, depending on how much of it there is. The article 'Effect of increased suspended sediment on suspension-feeding shellfish' explains why.

Read our Water & Atmosphere article 'Effect of increased suspended sediment on suspension-feeding shellfish'

Most shellfish are suspension feeders, meaning that they suck in water and filter out particles that, until sucked in, were suspended in the water column. Some of these particles are organic in origin and so have value as food. These are ingested. Other particles are mineral in origin (silt or “dirt”), have no food value, and so are excreted. We can deduce two things from this. Firstly, a certain amount of SPM is required for shellfish to survive, for if the water column is perfectly clear, then there will be no food and the shellfish will starve. Secondly, some portion of the SPM must have food value or, again, the shellfish will starve.

Here, then, is where increased turbidity levels (more precisely, increased concentrations of SPM in the water column), which are characteristic of estuaries within disturbed catchments, can have an effect: the increased supply of fine mineral silt that is eroded from the catchment reduces the ratio of edible to inedible particles suspended in the water column, and the shellfish have to work harder at filtering to feed themselves. The more energy they spend on feeding, the less they have available to grow and reproduce, which can lead to loss of condition and, ultimately, death. 'Modelling the effects of muddy waters on shellfish' shows how this works: there are different optimum levels of SPM for different species of shellfish.

Read our Water & Atmosphere article 'Modelling the effects of muddy waters on shellfish'

Increased turbidity also reduces light levels, which can reduce primary production, including the growth of phytoplankton (which fuels the estuarine food web) and “macrophytes” such as seagrasses. In addition, lower water clarity can reduce the ability of visual predators (such as snapper) to hunt.

Here is where we see what “effects-based management” under the Resource Management Act really means: if some proposed landuse change is going to result in levels of SPM in an estuary exceeding the level that is known to be harmful to shellfish, then the proposed landuse may be denied consent because it will have an adverse effect (on the shellfish). The proposer is free to take steps to reduce the adverse effects, by installing settling ponds to trap silt runoff while a road is being built, for instance. Remember, the RMA intends us to manage on the basis of effects, not the activities per se that cause those effects.

Find out more about the Resource Management Act

So, how can we know if a proposed landuse is going to change SPM levels in an estuary? This is what models are for.

Find out more about models

Sediment slugs

When it rains, soil is eroded from the catchment, washes into streams and rivers, and makes its way down to the coast, where it is dispersed and ultimately deposited. If the conditions are right, then some part of that load of eroded sediment may deposit in a noticeably thick “slug” in some parts of the estuary. If the slug is thick enough and covers a wide-enough area, then estuarine plants and animals unlucky enough to be under the slug can be smothered and killed. This process is natural enough, but, like many natural processes, can be magnified in estuaries that sit within disturbed catchments.

Quite a few factors must come together for a sediment slug to be deposited, but it is not impossible. For example, discharge of freshwater containing a large sediment load generally needs to occur on an incoming tide, so that sediment is not immediately flushed out to sea. The slug usually can only occur in a sheltered part of the estuary, where waves are not able to wash it away. Finally, the water depth will be fairly shallow so that suspended sediment does not have too far to settle down to the bed.

NIWA scientists have conducted a series of experiments that involved depositing artificial slugs of sediment to determine the effect of the slug on the underlying flora and fauna and how recovery occurs.

In time, the slug may be washed away by waves and currents or mixed down into pre-existing sediments by bioturbating creatures like crabs. Rehabilitation will depend on these factors and the availability of colonising animals (see, for instance, 'Winds, waves, and recovery from sedimentation in estuaries'). If this kind of thing happens too often, or slugs cover a wide enough area, then there may be a long-term shift in the estuary sediments and its ecology.

Read our Water & Atmosphere article 'Winds, waves, and recovery from sedimentation in estuaries'

'Sediment dumps in estuaries: filling in gaps with a risk map' is a step-by-step guide to identifying estuaries and parts of estuaries that are prone to this kind of impact, by looking for key dump signs, threat indicators and ecological changes.

Read our Water & Atmosphere article 'Sediment dumps in estuaries: filling in gaps with a risk map'

'Assessing human impacts on estuaries: it’s a risky business' describes a model that has been used by regional authorities to estimate risk of sediment slugs occurring during the earthworking phase of greenfields development. This phase of development is particularly targeted for two reasons. Firstly, it is when soils, which lie naked before the elements, are most liable to erode. Secondly, it is relatively easy to take steps to reduce the vulnerability of the soils. For instance, silt fences can be installed, unstable slopes can be ruled out of bounds for development, and slopes can be grassed and left alone during the wet season. So, here we have a potential problem, and potential solutions to that problem. How, then, is a risk assessment used in this kind of situation?

Read our Water & Atmosphere article 'Assessing human impacts on estuaries: it’s a risky business'

In the case of the greenfields development example, the developer needs to approach the authorities in advance (in order to gain consent) with a plan for how the greenfields are to be developed. The plan will include not only the final look of the development (lot size, housing density, road network, stormwater services and so on) but also how the development is actually going to be executed. This will include plans for things like staging the development, building access roads, and controlling erosion during earthworking. As part of the consenting process, the model is applied to estimate risk of sediment slugs occurring during the proposed development. If the risk is considered to be too high, the developer can be required to alter the plans. The process of putting forward a proposal and assessing its ecological consequences may be iterated until a plan with acceptable ecological risk can be found.

It is worth noting at this point that, because rehabilitation of impacted habitats and the communities they support is difficult, prevention of damage in the first place remains the best option. You might as well carve that statement in stone: it’s always true.

Change in substrate

In disturbed catchments, the balance between fine sediments (eroded from the land) and marine sands (swept in through the mouth of the estuary by waves and tides) is tipped in favour of the former, with the result that bed sediments of the estuary get muddier. The ecology changes as a result.

'How will habitat change affect intertidal areas in estuaries?' describes how most species have habitat preferences when it comes to how muddy the bed sediments are. For example, the mud crab is more likely to occur in areas with a high mud content; cockles prefer little mud; and the polychaete worm Boccardia syrtis likes the middle ground (but other polychaetes get on fine in muddier sediments).

Read our Water & Atmosphere article 'How will habitat change affect intertidal areas in estuaries?'

This kind of information rings alarm bells, for it tells us how the ecology – particularly abundance and distribution of sediment-dwelling animals such as shellfish, polychaete worms, crabs, snails and anemones – are going to change in response to a long-term change in sediment type that is characteristic of estuaries in disturbed catchments. It is worth noting that when we seek to limit immediate impacts, such as those associated with sediment slugs that get deposited in the aftermath of rainstorms, then we are also reducing the rate, over the long term, at which bed sediments become muddier.

Urban contaminants

A page on the Ministry for the Environment’s website notes, ironically, that “Lead was first added to petrol in the 1920s as a cheap and convenient method of boosting octane (which enhances fuel combustion) and reducing engine 'knock' (caused by faulty combustion). The General Motors research engineer who made the discovery, Thomas Midgley, went on from this triumph to develop a non-toxic, non-flammable alternative to ammonia as a refrigerant – chlorofluorocarbon or CFC. Today, both of these substances are recognised as major pollutants.”

'Society's Responses to Air Pollution', Ministry for the Environment website →

When it rains, zinc is leached from galvanised iron roofs (by design), gets washed into stormwater drains, and for the most part attaches itself to fine sediment particles that are also travelling in the runoff. The sediment with its attached zinc load makes its way down to the coast where it is dispersed and, ultimately, deposited. If the zinc in the deposited sediments reaches a certain high concentration, then it can be toxic to the biota (see 'SWAT’s up Doc?').

Read our Water & Atmosphere article 'SWAT’s up Doc?' (PDF 1.1 MB)

Zinc, of course, is just one type of urban contaminant, with others being copper (from abrasion of car brake pads), lead (from lead-based petrol) and polycyclic aromatic hydrocarbons (from the inevitably incomplete combustion of hydrocarbons). These are “big problems” and, as such, require “ big solutions”, such as the banning of the sale of leaded petrol in 1996, after a long process that began in the mid-1980s. This, by the way, has already resulted in widespread reduction in lead concentrations in estuarine sediments.

Find out more about "big solutions"

Invasive species

Some nuisance and pest species invaded; others were invited. An example of an invited species is cordgrass (genus Spartina), which was planted in estuaries in many parts of New Zealand in the early 20th century to prevent shoreline erosion and as part of reclamation schemes to extend pastures. It has since established quite successfully, forming islands that stand above the intertidal flats in some areas, and dense barriers along the shoreline in other areas. The Department of Conservation and some regional councils have programmes to eradicate Spartina by spraying with Gallant, which is a herbicide that acts on grasses, but not on native species such as mangroves.

With the rise of international trade and travel, and widespread decline in the resilience of native ecosystems, other species have truly invaded.

'New alien mudworm now becoming a pest in longline mussels' describes a shell-boring polychaete worm, Polydora haswelli, that damages the shell of the green-lipped mussel, making it less attractive – and in some cases repellent – to consumers. It came to scientists’ attention in mid-2003 after worm-inhabited blisters were found inside the shells of farmed green-lipped mussels, although it has probably been in the country at least since the mid-1990s. It is not clear how it got here, although the best bet is via ship ballast water, which is discharged offshore before entering port to load. Native shell-borer worms do exist, but are not capable of damaging the hard, shiny green-lipped shell.

Read our Water & Atmosphere article 'New alien mudworm now becoming a pest in longline mussels'

The Asian kelp Undaria pinnatifida invaded in the late 1980s, arriving in ballast water in ships from Asia. Given its success so far – it is found widely throughout southeastern New Zealand – and the fact that its impacts vary from location to location, management is focused on slowing its spread around the mainland and, particularly, reducing its ability to penetrate remote regions and areas of special significance such as Fiordland and Abel Tasman National Park. This is being achieved by educating people on how to avoid spreading the kelp when moving boats and marine-farming equipment, investigating ways of treating boats and equipment, and operating early-detection and surveillance systems.

Some invaders may be riding on the back of climate change. For example, the southern saltmarsh mosquito (Ochlerotatus camptorhynchus), which is a tropical beast known to carry a number of viruses including that responsible for Ross River fever, has been found around the Kaipara Harbour. The Department of Conservation believes the mosquito arrived on vessels from Australia, and was able to withstand border fumigation control that is targeted at freshwater container-breeding mosquitoes, not saltmarsh species.

Vigilance is the key to protecting New Zealand’s biosecurity. The Department of Conservation website gives an account of who is involved in guarding our borders, the law pertaining to this, international treaties and obligations, how the defences work, and the role and duties of the individual in keeping our borders secure. (Go to the DOC website and follow the trail to “Guarding the Borders”.) Information on some of the technical aspects of surveillance and reporting can be found at NIWA’s National Centre for Feshwater and Estuaries).

DOC website →

National Centre for Freshwater and Estuaries

Faecal contamination

As noted in 'Flood flushing of bugs in agricultural streams', pastoral agricultural streams in New Zealand are chronically contaminated by livestock faeces. These may be washed by rainfall from pastures into streams, or deposited directly into streams by animals, where they come to be bound up with the streambed sediments. However, those same streambeds are disturbed by floods or livestock trampling, which mobilises the sediments and their attached faecal contaminants, sending them on their way down to the coast. Here, they can be a danger, since faeces of all warm-blooded animals – which includes us – can contain disease-causing micro-organisms (or “pathogens”).

Read our Water & Atmosphere article 'Flood flushing of bugs in agricultural streams'

A pathogen is a disease-causing micro-organism. Pathogens include bacteria (e.g., Camplylobacteria, Leptospira, Salmonella, Yersinia enterocolitica), viruses (hepatitis A and E) and parasites (Giardia, Cryptosporidium).

Agriculture is a “diffuse source” of faecal contamination; other diffuse sources include wild animals (for instance, possums and deer) and birds. “Point-source” faecal contamination comes from piped discharges of treated and untreated effluent, including domestic sewerage, and abattoir and farm waste.

It is difficult and expensive to screen water samples for the presence of pathogens, and so screening for more-easily detectable “indicator species” is done instead. For instance, Environment Waikato routinely monitors a number of coastal swimming beaches for enterococci (a bacterium that lives in animal guts) for an indication of whether water quality is suitable for swimming. Suspension-feeding organisms such as shellfish (the ones that feed by filtering suspended particles from the water column) are a problem here, since filter-feeding causes micro-organisms to accumulate in the flesh of the animal. Although not necessarily harmful to the shellfish, these can be very harmful to a human consumer of the shellfish. Different indicators may be used, and different standards applied, for assessing contamination of shellfish beds.

As far as agricultural diffuse-source contamination goes, the best mitigation strategy is fencing to exclude livestock from streams, which precludes direct deposition of faeces into waterways and trampling. Planting riparian buffer strips is also a good option, since these can trap sediments and faecal microbes in overland flow that would otherwise make their way into waterways.

Bottom line

If you are really paying attention here, you will notice that most problems in the estuary start “when it rains”. Why? Remember, estuaries are at the bottom of the freshwater drainage network, which means that “what ails our estuaries” often comes from the land, carried down streams and rivers by rainwater.


Whaingaroa (Raglan) estuary. [Alastair Senior]


Measuring mangrove growth. [Anne-Maree Schwarz]


[Don Morrisey]


[Simon Thrush]


Mudbank. [Malcolm Green]


Mixing waters. [Alan Blacklock]


Spartina eradication by spraying with herbicide. [Andrew Swales]


A new goby species, Acentrogobious pflaumii, was recently discovered in Whangapoua Harbour, Coromandel. The most striking feature of the new species is the many iridescent blue spots along its sides, which the native goby does not have. [Rudi Kuiter]


Unprotected stream in a cow paddock. [Alan Blacklock]