The Plight of New Zealand’s Freshwater
Biodiversity
Elston E., Anderson-Lederer R., Death R.G. and Joy M.K.

August 2015
Conservation Science Statement No. 1

 Authors: Elston E.1 , Anderson-Lederer R.1, Death R.G.2 and Joy M.K.2
1
Society for Conservation Biology (Oceania), New Zealand
2
Institute of Agriculture and Environment-Ecology, Massey University, Private Bag
11-222, Palmerston North New Zealand
Citation
Elston E., Anderson-Lederer, R. Death R.G., and Joy M.K. (2015). The plight of
New Zealand’s freshwater species. Conservation Science Statement No. 1,
14pp. Society for Conservation Biology (Oceania), Sydney.
This Conservation Science Statement was peer reviewed and is endorsed by:
Dr Gerry Closs, Associate Professor, University of Otago
Prof Jenny Webster-Brown, Director, Waterways Centre for Freshwater Management, Canterbury University
Dr Marc Schallenberg, Research Fellow, University of Otago
Paul Boyce, Researcher, Massey University
Corina Jordan, Environmental Manager, Fish and Game New Zealand
Prof Jon Harding, Professor, University of Canterbury
Dr Bruno David, Freshwater scientist
Trent Bell, EcoGecko Consultants
Tamsin Ward-Smith, Cape Sanctuary
Kyleisha Foote, Freshwater Scientist, Massey University
2
Dr Cynthia Winkworth, NZ FRS&T Postdoctoral Fellow, University of Otago

Front cover photo of Lake Rotoiti, Nelson Lakes National Park, courtesy of Amanda Taylor

 Contents
Executive Summary ............................................................................................................................. 4
The importance of freshwater ecosystems ...................................................................................... 5
Status of rivers, lakes, estuaries, wetlands, ponds and their biodiversity ................................... 5
Drivers of freshwater species decline ............................................................................................... 8
The future of freshwater biodiversity ................................................................................................. 9
The way forward for our freshwater biodiversity............................................................................ 10

3

 Executive Summary
New Zealand’s freshwater habitats including rivers, lakes, estuaries and other wetlands;
groundwater and geothermal ecosystems support a unique array of flora and fauna.
Freshwater is New Zealand’s greatest asset and is a taonga of paramount importance. It is
valued for its contribution to biodiversity, recreation, the economy and overall well-being of
New Zealanders. It is also a vital element of whakapapa and provides valuable resources
such as mahinga kai (indigenous freshwater species that have traditionally been used as
food, tools, or other resources), and underpins the country’s ever-growing tourism industry.
Reinforcing this importance, New Zealanders consider water quality to be the most important
environmental challenge facing New Zealand1.
This Conservation Science Statement uses the latest scientific understanding of New
Zealand’s unique freshwater ecosystems (rivers, lakes, other wetlands, groundwater
ecosystems) to propose how effective policy and management based on scientific evidence
can safeguard their future for generations to come. We identify six clear priorities to protect
New Zealand’s freshwater biodiversity:
1. change legislation to adequately protect native and endemic fish species and
invertebrates, including those harvested commercially and recreationally;
2. protect habitat critical to the survival of New Zealand’s freshwater species;
3. include river habitat to protect ecosystem health in the National Objectives
Framework for the National Policy Statement on freshwater;
4. establish monitoring and recovery plans for New Zealand’s threatened freshwater
invertebrate fauna;
5. develop policy and best management practices for freshwater catchments which
includes wetlands, estuaries and groundwater ecosystems and;
6. establish, improve and maintain appropriately wide riparian zones that connect
across entire water catchments.

4

 The importance of freshwater ecosystems
Freshwater lakes, rivers, estuaries, groundwater systems and other wetlands provide a
range of ecosystem services for people and support a diverse array of other life. They are
valued for their contribution to biodiversity, recreation, the economy and overall well-being.
Across the globe more than 44,000 described species live in freshwater ecosystems, even
though these ecosystems cover only 1% of the Earth’s surface2.
New Zealand’s freshwater ecosystems are an important part of whakapapa and provide
valuable resources such as mahinga kai (thinking, involving and understanding the
simultaneous protection and use of resources). More than 770 lakes and innumerable ponds
cover around 3400 square kilometres3. These lakes feed into 70 major rivers systems and
hundreds of streams, and support other ecologically important ecosystems, including 73
nationally significant wetlands4.
These freshwater ecosystems also support a unique flora and fauna. There are 66
freshwater fish species in New Zealand, with 31 only found on our islands (endemic)5. Half
of these species spend some part of their lives at sea, including eels and whitebait which
have important cultural and recreational values. There are at least 638 species of
invertebrate found nowhere else and many more still to be discovered. There are also 38
endemic species of water plants and about 34 species of waterbirds6.
So far, six wetlands of international importance or Ramsar wetland sites have been
recognized in New Zealand, covering 39,068 ha. These sites are recognised for their unique
cultural and biological significance. Historically, they provided Maori with food (particularly
waterbirds, eels and other freshwater fish), taro cultivation, harakeke (flax) for weaving and
other materials for medicinal, food, building, and craft use. There are five endemic mudfish
species in New Zealand and four of them evolved to specifically occupy different wetland
habitats7,8. Wetlands also provide feeding grounds for migratory shorebirds that move to
New Zealand during the Northern Hemisphere winter.

Status of rivers, lakes, estuaries, wetlands, ponds and their
biodiversity
There is growing evidence that freshwater ecosystems are degrading, more so than marine
and terrestrial ecosystems, contributing to the biodiversity crisis9,10,11,12. In 2009, the
International Union for the Conservation of Nature’s (IUCN) Red List of Threatened Species
listed 37% freshwater species as extinct or threatened around the world13. While alarming,
these trends probably underestimate the true decline of freshwater species, due to
insufficient data in many parts of the world. This problem is nowhere more prominent than in
New Zealand’s rivers, lakes and wetlands. For example, more freshwater fish species are
under threat than ever before and increasing development, expansion of introduced fish and
demand for water is increasing the threat ranking for many species and pushing some
nationally critical species closer to extinction. The number of threatened or at risk species of
freshwater invertebrate has increased from 17 in 2005 to 82 in 2013, and we have
insufficient data to evaluate the other species.

5

 The status of New Zealand’s freshwater has become an issue of national significance. Over
the past 25 years, New Zealand has experienced rapid intensification of lowland agriculture
and increased urbanisation. This has resulted in an alarming decline in the quality of
freshwater for both native biodiversity and human well-being. Water quality has consistently
declined in the 77 National Water Quality Monitoring Sites (NRWQN), monitored since 1990,
particularly in lowland rivers41. Further, 96% of the sites in 300 lowland pastoral catchments
and all of the sites in urban catchments, monitored by local government, failed the pathogen
standard for safe swimming and more than 80% of these sites exceeded nutrient guideline
levels15.
Lakes and groundwater ecosystems parallel these declines in water quality. Thirty-two
percent of monitored lakes are now classed as polluted with nutrients, or 84% of lakes in
pastoral catchments 16. In groundwater ecosystems, nitrate levels are rising at 39% of
monitored sites and groundwater pathogen levels exceed human drinking standards in 21%
of monitored sites17.
What is eutrophication?
Eutrophication occurs when water bodies
(e.g. lakes) become enriched with
nutrients. Nutrients run-off into waterways
and cause phytoplankton to grow rapidly,
producing algal blooms. These suffocate
marine and freshwater organisms by
using up all the oxygen. Nitrates and
phosphates are the most common
nutrients responsible for algal blooms in
New Zealand.

Fig. 1. Green algal bloom in a small freshwater lake in New Zealand (photo courtesy of Rob
Suisted Photography).
Freshwater biodiversity has declined over the past century, at particularly fast rates over the
last 40 years. Proportionally, New Zealand has more threatened freshwater species than
most countries around the world18. While only one native fish species is extinct, many are
locally extinct throughout New Zealand. Numbers of all aquatic species listed as threatened
have grown over the past 20 years, accounting for changes in criteria for risk assessments
(Fig. 2). The New Zealand Department of Conservation recorded 10 species of freshwater
fish species as threatened in 1990; by 2002 the number rose to 16 species19. Under the
2013 New Zealand classification, 74% of all native freshwater taxa and 76% of all nondiadromous taxa (i.e. confined to fresh water) are considered threatened or at risk19,20.

6

 Fig. 2. Changes in percentage of threatened native freshwater fish in New Zealand, 1992 –
2013, based on IUCN data.
New Zealand’s freshwater species are also threatened by several other factors, including
invasive species21. Twenty-one introduced species of freshwater fish have established selfsustaining populations in New Zealand22. Exotic fish species outcompete or prey on native
fish species. Also, invasive exotic plants threaten native species. Over 70 freshwater
introduced aquatic plants are silently invading water ways.
In the last 150 years, 90% of New Zealand’s wetlands have been drained. Even though
wetlands are identified as ecosystems of national importance in the Resource Management
Act (RMA), wetland loss has been exacerbated with recent intensification of farming, along
with the effects of urbanisation and introduction of exotic species. These cumulative impacts
have increasingly degraded water quality and ecosystem health and led to the decline of
numerous native freshwater species.
Dams, levees and channels also cause major ecological problems to New Zealand’s rivers
and wetlands23. In addition to the habitat alteration of vulnerable species such as the banded
plover (Charadrius bicinctus), New Zealand dabchick (Poliocephalus rufopectus) and blue
duck (Hymenolaimus malacorhynchus) through waterway alteration, native fish that
complete part of their life cycle at sea are particularly vulnerable to man-made barriers.
Additionally, fish adapted to high water flows, such as the Torrentfish (Cheimarrichthys
fosteri) (Fig. 3), can be negatively impacted when too much water is removed for irrigation24.

7

 Fig. 3. Torrentfish (Cheimarrichthys fosteri) only live in rapid flowing water (i.e. torrents).
These fish are threatened by the diversion of water and building of dams, decreasing high
water velocity on which they depend (photo courtesy of Rob Suisted Photography).

Drivers of freshwater species decline
Around the world and in New Zealand, there are ubiquitous threats to freshwater
ecosystems including loss and degradation of habitats, caused by river regulation and
diversions of fresh water, pollution, overharvesting, invasive species, disease and climate
change. Invasive species, deteriorating water quality and reduced habitat remain the biggest
threats to New Zealand’s native freshwater species.
Water quality in urban and rural areas is rapidly deteriorating, as agricultural land use
intensifies and urbanisation increases. Between 1987 and 2006, there was a 24% increase
in built-up urban areas in and around Auckland25. Along with this growth, the density of
people living on the land and their dwellings has increased (Fig. 4). Widespread urbanisation
has boosted pollution of freshwater bodies and the marine environment, initially through the
release of sediment during land clearing and earthworks, and later with heavy metals and
toxins such as polyaromatic hydrocarbons (PAHs) from rain and storm water runoff from
roads and unpainted galvanised roofs.
Most recently, diffuse pollution from more agricultural intensification in rural areas has
become the worst threat to freshwater ecosystems. Between 2003 and 2007, the median
levels of total nitrogen were five times higher in pastures than in native forests26, impacting
on runoff into rivers and wetlands. Increased stocking rates release fine soil particles,
nutrients and harmful bacteria into streams and rivers27. In addition to this, forest clearance
and poor management of erosion have also had major impacts on fish biodiversity28.

8

 Fig. 4. Urban growth around Auckland, 1996-2012 (extracted from the Land Cover Database
of New Zealand 2012).
Human activities also threaten New Zealand's remaining wetlands29 which continue to be
drained for urban or rural development. Governments and communities are also engineering
rivers to mitigate floods that reduce habitat diversity, changes water levels, and damages
existing vegetation, providing access for invasive species30. There is also reclamation of lake
and river margins, lagoons and estuaries, and draining of farm swamps. Wetlands are also
polluted by excess run-off of sediment and nutrients from farmlands. Stock grazing in
wetlands and surrounding catchments damages vegetation, decreases soil stability and
contributes to pollution and poor water quality.

The future of freshwater biodiversity
Governments and their committees continue to debate policies for the future management of
New Zealand’s freshwater ecosystems. Such policies significantly affect the viability of
different plants, animals and other organisms that depend on our freshwater systems. The
ecosystem services provided by our freshwater ecosystems are also critical to the quality of
life of many New Zealanders. There remain major inadequacies in our legislation, including
conflicting objectives, affecting sustainable management.
The Freshwater Fisheries Regulations (1983) formally protects introduced fish species such
as brown trout (Salmo trutta), rainbow trout (Oncorhynchus mykiss) and chinook salmon
(Oncorhynchus tshawytscha), but does not protect native fish species; the exception is the
New Zealand grayling (Prototroctes oxyrhynchus), which became extinct in 1930. There are
also significant information gaps regarding population status and ecology of native fish and
invertebrate species, resulting in a poor focus for policy and management. For example,
Total Allowable Catches (TAC) under the Fisheries Act 1996 allows for quotas to be
determined for native species despite insufficient information available to determine
Maximum Sustainable Yield (MSY).
9

 The New Zealand Government identified core priorities and objectives to improve freshwater
management in the National Policy Statement for Freshwater Management 2014 (NPS-FM
2014)31. This established guidelines for water quality, which are insufficient to protect
freshwater biodiversity32. One measure of freshwater ecosystem health is based on nitrate
toxicity levels, currently set too low to avoid chronic ecological effects on native invertebrates
and most native fish species.
Such short-term decisions carry long-term political and economic costs. For example, the
cumulative costs of attempting to clean-up current freshwater problems on the Waikato
River, the Whanganui River and Lakes Taupo and Ellesmere/Te Waihora, have already cost
taxpayers hundreds of millions of dollars. Current policies will create future financial costs for
generations to come but this need not occur.

The way forward for our freshwater biodiversity
As a signatory to the United Nations Convention on Biological Diversity, New Zealand is
committed to protecting biological diversity. There is sufficient scientific knowledge to
improve decision making. We provide the scientific rationale to improve conservation policy
and management of New Zealand’s freshwater ecosystems may prevent the further decline
of New Zealand’s remaining freshwater biodiversity.
1.

Change legislation to adequately protect native and endemic fish species and
invertebrates, including those harvested commercially and recreationally.

Under current freshwater reform, little attention has been paid to protecting native species.
Increasingly freshwater plants and animals are threatened, requiring changes to their
conservation status to higher levels of vulnerability. And yet, none of these freshwater
species have statutory protection. At least five threatened native fish are harvested
commercially and recreationally, without appropriate data to ensure sustainable
management. Only those native fish not used for ‘human consumption or scientific purposes’
are currently protected. Changes are required to the Freshwater Fisheries Act (1983) to
formally protect native species.
2.

Protect habitat critical to the survival of New Zealand’s freshwater species.

Many rare and range-restricted fish and invertebrates live in highly specialised habitats
including seeps, wetlands, springs and braided rivers, which are all increasingly threatened
by agriculture intensification and introduced species. Without formal protection of these
habitats through conservation or reserve status, some species will become increasingly
threatened and conceivably driven to extinction. Changes to the climate will also threaten
these often isolated and fragmented populations. Some species (e.g. pencil galaxias) are in
restrictive spring heads where no escape routes remain. For these species, a native fish
hatchery and a holding facility, in case of drought, should be established as a safety bank to
help manage these populations (as successfully implemented for birds on off-shore islands).

10

 3.

Include river habitat to protect ecosystem health in the National Objectives
Framework for the National Policy Statement on Freshwater Management.

The National Objectives Framework outlines key attributes to protect and/or restore the
ecosystem health of New Zealand’s waterbodies. However, there is no attribute to protect
species’ physical habitat. Water quality and quantity can be maintained to preserve
ecosystem health but, if there is no habitat for the animals to live, they will still not be able to
survive. We recommend that some measure of habitat quality (e.g. Natural Character Index)
be included as an attribute in the National Objectives Framework on its review in 2016. This
will ensure that all three key environmental variables for preserving ecosystem health (water
quality, quantity and habitat) are protected.
4.

Establish monitoring and recovery plans for New Zealand’s threatened
freshwater invertebrate fauna

The small invertebrates of New Zealand’s land and water are often overlooked in
conservation activities despite their obvious importance. Although the Department of
Conservation have recovery plans for some freshwater fish species we are not aware of any
similar plans for the 334 species of threatened, at risk, or data deficient aquatic invertebrates
(52% of the known fauna). In fact, there is as yet no coordinated monitoring plan to assess
trends and state in biodiversity within the conservation estate. Invertebrates, in particular are
largely over looked in conservation activities in New Zealand. We urgently need monitoring
and recovery plans for some of our aquatic invertebrates; they are just as important to New
Zealand as our fish, plants, and birds providing the food base for many important species.
5.

Develop policy and best management practices for freshwater catchments
which includes wetlands, estuaries and groundwater ecosystems.

There is currently no policy for wetlands, estuaries and groundwater ecosystems. There is
little information on water quality limits for these areas and no clear national priorities for
conservation of these hotspots of biodiversity. This is despite their importance and value to
communities and the environment. Managing nutrients requires a whole catchment
approach, but this is not included in current frameworks. Current nutrient limits for nitrogen
and phosphorus in rivers far exceed the levels that would safeguard aquatic ecosystems
from the effects of algal blooms. An independent review should be carried out of current
freshwater frameworks and their effectiveness in addressing degradation of wetlands,
estuaries and groundwater. This can underpin potential solutions that mitigate impacts on
the health of the entire aquatic ecosystem.
6.

Establish, improve and maintain appropriately wide riparian zones that connect
across entire water catchments.

Riparian management can improve both water quality and habitat for aquatic life but success
depends on connectivity. Rehabilitation of streams can be effective if riparian planting begins
from the headwaters and progresses down through the catchment to produce a long and,
continuous buffer. These riparian zones also need to be permanently protected and
maintained. At present, the development of riparian zones is ad-hoc and voluntary. There is
a need for national guidance to prioritise rehabilitation and ensure the inter-connectedness
of planting, fencing and other restoration activities. In particular this should focus on small
11

 headwater streams where the greatest biodiversity often occurs and where sediments and
nutrients first enter streams to flow downstream.

References
1. Hughey, K.F.D., Kerr, G.N. and Cullen, R. (2013). Public perceptions of New Zealand’s
environment: 2013. EOS Ecology, Christchurch.
2. Reaka-Kudla, M.L. (1997).The global biodiversity of coral reefs: a comparison with rain forests. In
‘Biodiversity II: Understanding and protecting our biological resources’. (Eds M.L. Reaka-Kudla,
D.E. Wilson and E.O. Wilson, pp. 83-108.Joseph Henry Press, Washington, D.C., USA.
3. Anon. (2000).The New Zealand biodiversity strategy: our chance to turn the tide. Department of
Conservation and Ministry for the Environment. Wellington.145p.
4. Cromarty, P. and Scott, D. (1995). A directory of wetlands in New Zealand. Department of
Conservation. Wellington.
5. Ministry for the Environment (1997). State of New Zealand’s Environment 1997. Ministry for the
Environment. Wellington.
6. Joy, M. and Death, R.G. (2013). Freshwater biodiversity. In ‘Ecosystem services in New Zealand:
conditions and trends’. (Ed. J. R. Dymond). pp. 448-459. Manaaki Whenua Press, Lincoln, New
Zealand.
7. Johnson, P.N. and Brooke, P.A. (2009). Wetland plants in New Zealand. Manaaki Whenua Press,
Canterbury, New Zealand.
8. Suren, A. and Sorrel, B. (2010). Aquatic invertebrate communities of lowland wetlands in New
Zealand. Department of Conservation. Wellington.
9. Millennium Ecosystem Assessment (2005). Ecosystems and Human Well-being: Synthesis. Island
Press, Washington, DC.
10.Ricciardi, A. and Rasmussen, J.B. (1999). Extinction rates of North American freshwater fauna.
Conservation Biology 13: 1220-1222.
11. Foley, J.A., DeFries, R., Asner, G.P., Barford, C., Bonan, G., Carpenter, S.R., Chapin, F.S., Coe,
M.T., Daily, G.C., Gibs, H.K., Helowski, J.H., Holloway, T., Howard, E.A., Kucharik, C.J.,
Monfreda, C., Patz, J.A., Prentice, I.C., Ramankutt, N. and Snyder, P.K. (2005). Global
consequences of land use. Science 309: 570-574
12. Dudgeon, D., Arthington, A.H., Gesssner, M.O., Kawabata, Z.I., Knowler, D.J., Leveque, C.,
Naiman, R.J., Prieur-Richard, A.H., Soto, D., Stiassny, M.L.J. and Sullivan, C.A. (2006)
Freshwater biodiversity: importance, threats, status and conservation challenges. Biological
Reviews 81:163-182.
13. IUCN (International Union for the Conservation of Nature) (2010). The IUCN Red List of
Threatened Species. http://www.iucnredlist.org
14. Ballantine, D.J. and Davies-Colley, R.J. (2010). Water quality trends at NRWQN sites for the
period 1989-2007. National Institute of Water and Atmospheric Research Ltd.
15. Larned, S.T., Scarsbrook, T.H., Snelder, N.J., Norton, N.J., and Biggs, B.J.F. (2004). Water
quality in low-elevation streams and rivers of New Zealand: recent state and trends in contrasting
land-cover classes. New Zealand Journal of Marine and Freshwater Research 38:347-266.
16. Verburg, P., Hamill, K., Unwin, M. and Abell, J. (2010). Lake water quality in New Zealand 2010:
status and trends. National Institute of Water & Atmospheric Research Ltd.
17. Daughney, C.J. and Wall, M. (2007). Ground water quality in New Zealand. State and trends
1995-2006. GNS Science Consultancy Report 2007/23.
18. Hitchmough, R., and Comarty, P. (2007). New Zealand threat classification system lists.
19. Allibone, R., David, R., Hitchmough, R., et al (2010). Conservation status of New Zealand
freshwater fish, 2009. New Zealand Journal of Marine and Freshwater Research 44: 271-287.
20. Goodman, J.M., Dunn, N.R. and Ravenscroft, P.J. (2013). Conservation status of New Zealand
freshwater fish, 2013. Department of Conservation. Wellington, New Zealand.

12

 21. Jones, P.E. and Closs, G.P. (2014) Life history influences the vulnerability of New Zealand
galaxiids to invasive salmonids. Freshwater Biology. doi: 10.1111/fwb.12637
22. Dean, T. (2010). Invasive freshwater fish in New Zealand: DOC’s present and future
management. Department of Conservation. Wellington.
23. Young, R.G., Smart, G. and Harding, J. (2004). Impacts of hydro-dams, irrigation schemes and
river control works. Freshwaters of New Zealand: 37-31.
24. McDowall, R.M. (1998). Fighting the flow: downstream-upstream linkages in the ecology of
diadromous fish faunas in West Coast New Zealand rivers. Freshwater Biology 40:111-122.
25. Auckland Regional Council (2010). State of the Auckland Region Report 2010. Auckland Regional
Council, Auckland.
26. Davies-Colley, R.J. (2014). River quality in New Zealand: an introduction and overview. In
‘Ecosystem services in New Zealand: conditions and trends. (Ed.J. R. Dymond). pp. 459-465.
Manaaki Whenua Press, Lincoln, New Zealand.
27. Quinn, J.M. and Stroud, M.J. (2002). Water quality and sediment and nutrient export from New
Zealand hill-land catchments of contrasting land use. New Zealand Journal of Marine and
Freshwater Research 36: 409-429.
28. McEwan, A.J. and Joy, M.K. (2011). Monitoring a New Zealand freshwater fish community using
passive integrated transponder (PIT) technology; lessons learned and recommendations for
future use. New Zealand Journal of Marine and Freshwater Research 45: 12-133.
29. Johnson, P. and Gereaux, P. (2004). Wetland types of New Zealand. Department of
Conservation. Wellington.
30. Death, R.G., Fuller, I.C. and Macklin, M.G. (in press) Resetting the river template: the potential for
climate-related extreme floods to transform river geomorphology and ecology. Freshwater
Biology.
31. Ministry for the Environment (2014). National policy statement for freshwater management.
Wellington. http://www.mfe.govt.nz/publications/fresh-water/national-policy-statement-freshwatermanagement-2014
32. Parliamentary Commissioner for the Environment (2015). Managing water quality: examining the
2014 National Policy Statement. Wellington.

13

 \4


Society for Conservation Biology

14