What are intermittently closed estuaries?

Beach Road Creek mouth
Parson’s Creek mouth

Most people understand the difference between lakes, rivers and estuaries. But "intermittently closed estuaries" are not so well known.

When freshwater flows into an area that is partially enclosed, but can still reach the sea, the water becomes brackish. This area of water which is not quite fresh water but not quite saltwater is an estuary. Freshwater flows into the area, time tidal waves bring seawater into the area, and then the mixed brackish water to flows back out into the sea.

In some rivers, the water flow slows down or stops for periods of time (like during dry summers). But while the freshwater slow slows or stops, the ocean waters are still pushing sand and pebbles into the area. This can cause the mouth of the river to become blocked, closing the estuary. These types of estuaries are called intermittently closed estuaries (ICEs).

Other names for intermittently closed estuaries (ICEs) include:

  • intermittently closed and open lakes/lagoons or ICOLLs
  • barrier bar lagoons
  • Waituna-type lagoons
  • hapua

Both an ICE and an open estuary have a barrier of some type which slows the flow of water into a sea. The key difference is that in an ICE is barrier is sometimes blocked, preventing flow to the sea.

Names of different types of estuaries

Intermittently closed estuaries are special waterbodies in many ways. But a main interest is that they can have two very different states:

  1. an open estuary when the barrier bar is open and
  2. a lake- or lagoon-type waterbody when the barrier bar is closed

Each state causes different surface areas, water depths, water levels, salinities, and biological communities. Meaning, ICE can act as two different coastal habitats, depending on the state of the barrier bar.

Kurinui - showing the cutting through of a barrier bar by outflow

Barrier Bars

An estuary forms when sea water mixes with fresh water flowing from the tidal part of a river. On some parts of the coast, the sea can push natural material like sand, gravel, and shingle into the mouth of the estuary. This temporarily blocks the river flow, creating a lagoon, and the water level rises. The blockage is known as a barrier bar.


Barrier bars can be made of shingle, pebbles, coarse sand, fine sand, and gravel (and are usually a mixture of these). Coarser materials allow water to easily seep through the barriers. Whereas finer barrier bar materials can prevent the mixing of sea water and river water.

ICE Cycle

Barriers tend to close when freshwater outflows* are low (we see this during droughts and during summer). Storms at sea and strong currents can push barrier materials up onto the beach, blocking off the outflow. At this point, the water levels in the backed-up estuary (lagoon) rise.

Once high enough to go over the barrier, the water pressure flowing across the bar makes a cut in the barrier and re-opens the estuary. In intermittently closed estuaries, this cycle of blockage and opening is repeated over and over.

In general, barrier bars open naturally when freshwater inflows* to the ICE are high (we see this during floods and often during winter). The rising water level overtops the barrier bar and then cuts down into it, releasing more water to the sea. When the tide is out, most of the water in a lake/lagoon can drain out through an open barrier.

Substrates - barrier bar materials

Otago's ICEs

A recent survey has identified 24 important ICEs along Otago's coastline. Some are already well known:

  • Kakorai Lagoon,
  • Tomahawk Lagoon,
  • Anderson's Lagoon, and
  • Hawkesbury Lagoon.

Some ICEs, such as Kaikorai, Tomahawk and Hawkesbury, are artificially opened to allow the water to drain out. The Otago Regional Council grants consents for this work in order to reduce the risk of rising water levels from threatening homes, roads, farmland, and other infrastructure. However, many of Otago's ICEs are small and are often overlooked.

What lives in Otago's ICEs

Intermittently closed estuaries are home to a range of plants, invertebrates, birds and fish. Some species spend their whole lives in ICEs (they are residents). While other species, such as eels/tuna, whitebait/inaka, and flounder/pātiki, are itinerant species.

Organisms living in Otago ICE habitats must be able to adapt to the highly variable water levels and salinities found in ICEs. This includes a variety of waterfowl, waders, migratory fishes, estuarine invertebrates, and salt tolerant plants.

Thriving in the distinctive environment of an ICE

The environment of an ICE can be difficult due to:

  • water levels moving between extreme highs and lows
  • differing levels of salinity (the amount of dissolved salt in the water)
  • an intermittent connection to the sea

This unique environment of ICEs provides a refuge habitat that some native species can tolerate and can thrive in. This includes several of Otago's threatened species. The environment also helps prevent potential invasive species from getting established.


Species in an intermittently closed estuary

The value of Otago's intermittently closed estuaries

Apart from being a home to a variety of organisms, many of which are endangered, ICE are valued in other ways.

From an environmental view, an intermittently closed estuary can act as a water filter protecting our oceans. ICEs can trap and transform contaminants and pollutants before they enter the sea. For example, the plant nutrient nitrate can be microbially transformed in the ICE environment, converting it to inert N2 gas by a process called denitrification.

In addition, some New Zealand ICEs are important mahinga kai/mahika kai sites. They are culturally important areas where food and resources are gathered, so are cared for by mana whenua. 

Furthermore, many people value ICEs for recreation (e.g., dog walking, bird watching, fishing, etc.) and for their ever-changing scenic beauty.

Living in harmony with ICEs

A eutrophic ICE, showing abundant mats of macroalgae

Many of our activities impact the biodiversity of ICEs and the values that we derive from ICEs. The main impacts from urban encroachment, land reclamation, wetland drainage, artificial opening regimes, and nutrients and contaminants that we discharge into them via poor land management, stormwater, and sewage effluent. These pressures can manifest as algal blooms, toxic cyanobacteria blooms, oxygen depletion in the waters, rapid sediment infilling, loss of fringing wetlands, changes in the balance between freshwater and sea water, and the loss of species due to these stressors.

Paying attention to what lives in the lake/lagoon phases can provide an idea of the health of the ICE. Submerged plant species are particularly sensitive to nutrients, suspended sediments and ecological degradation. In ICEs, plants like seagrasses (Ruppia sp.) and muskworts (charophytes) absorb nutrients (suppressing algal blooms), oxygenate the water, and provide habitat for fish and intertebrates. These are also food for waterfowl, attracting swans and ducks to ICEs when these plants are abundant. So, Ruppia and carophytes are sensitive indicators of the health of ICEs.

If you notice them, then the ICE is likely to be in a good condition. On the other hand, if they are absent, the ICE may be in a degraded state.

Monitoring intermittently closed estuaries in Otago

Otago’s ICE’s are valuable, often overlooked habitats. But they are complex and unfortunately, some are degraded due to our activities. The Otago Regional Council is developing a monitoring programme for some of the most important ICEs.

Monitoring will focus on key indicators of the health of the ICEs. This will allow the council to assess the current health of Otago’s ICEs and their health trends into the future. ORC currently monitors the water quality and health of the inflows to a number of the ICEs. However, it is now developing a monitoring programme focused on the ICEs, themselves. Monitoring will include regular measurement of water quality, water level, state of the barrier bar, oxygen status of the bed, and levels of algae.

The council will then report its findings to the public in regular state of the environment reports.

Otago Regional Council scientist measuring water quality at Parsons Creek ICE, Oamaru

Management of Otago's ICE

The Otago Regional Council is responsible for helping to maintain and improve the health and values of Otago’s ICEs. While some ICEs are currently in a good condition, others need improvement.

The main problem that can occur is that the ICE can become eutrophic – a condition where there is excessive algal growth. Too much plant and algal growth in an ICE can lead to a loss of dissolved oxygen from the water and bed of the ICE. This can happen when the plant material dies and decomposes, or during the nighttime when all the plants and algae undergo respiration, consuming oxygen from the water.

Issues with an eutrophic ICE

This condition looks unsightly, but more importantly, it is also toxic for many of the species in the ICE. Oxygen is necessary for fish, plants and invertebrates to survive. No oxygen present means these organisms must escape the ICE or die. At times, fish kills have been reported in some of Otago’s ICEs. A lack of oxygen also changes the water chemistry. This results in releasing potentially toxic levels of ammonia and hydrogen sulphide from the bed into the water column.

The key thing to avoiding eutrophication and fish kills is to make sure that plant nutrients (e.g., nitrogen and phosphorus) don’t get into the ICE. Some of the ways to make a difference to the ecological health of ICEs. include:

  • Improving farming practices in the catchment,
  • planting native vegetation along the banks of inflowing rivers, streams and creeks,
  • preventing stormwater and other urban/industrial discharges from getting into inflows

Another management tool that may help prevent algal blooms is the artificial opening of the barrier bar. This can allow the flushing of algae and nutrients out of the ICE. However, it has been found that in some ICEs, low water levels in the summer can encourage a build-up of algae and the worsening of symptoms of eutrophication.

Citizen Science

Along with the Otago Regional Council, the Department of Conservation, and Otago Fish & Game being involved in management of some of Otago’s ICEs, community groups have also formed and they play an active role in raising awareness of their local ICEs, undertaking restoration, carrying out environmental monitoring, and communicating information with the wider community.

One group is the Tomahawk Lagoon Citizen Science group, which is made up of intermediate and high school students, retired persons, school teachers, scientists, and other enthusiasts. This group has been collecting high quality water quality and biodiversity information on the Tomahawk Lagoons and their catchments since 2016. Their work has informed the Tomahawk Lagoons Catchment Group, which is working with the council to develop a management plan for the lagoons.

Some of the locals at Hawkesbury Lagoon have also organised themselves into a charitable trust called Hawkesbury Lagoon Incorporated. This group is involved with collecting information about the lagoon and its catchment and working with council to restore and better manage the lagoon.

Both these groups have excellent websites and the groups encourage people from the community to get in touch and get involved in restoring and safeguarding the special lagoons.

Interactive Map

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Reports and Publications

Intermittently closed estuaries are still under-researched, but Otago Regional Council is working to release research and findings on these vital parts of the Otago environment.

Page last updated 19 June 2024.