Scope
All freshwater ecosystems (such as streams, lakes, wetlands, geothermal systems and underground aquifers) and the freshwater species within them. These waterbodies and ecosystems are interconnected with both land and estuarine and coastal ecosystems. 

Desired outcome for 2020 
The extent and condition of remaining natural freshwater ecosystems and habitats are maintained. Some degraded or scarce habitats, such as lowland river systems, important wetlands and riparian areas, are restored or increased in area. Intact natural freshwater areas are protected and their natural character is maintained. 

Human activities in catchments are managed in an integrated way, avoiding, remedying or mitigating the adverse effects of land and water use (including pollution and sedimentation) on freshwater ecosystems. All freshwater ecosystems support biological communities largely comprising indigenous species. Plant and animal pests are managed to prevent further spread, and eradicated where necessary, to protect threatened indigenous ecosystems and species. Introduced fish (including sports fish such as trout and bio-control species such as grass carp) and introduced game (such as ducks) are managed so that they do not pose threats to indigenous species of plants or animals. 

There have been no further human-induced extinctions of indigenous freshwater species. Threatened species are on their way to recovery within their natural habitat, or in temporary ex situ facilities where necessary. The harvest of indigenous and introduced freshwater species is sustainable and does not pose a threat to freshwater biodiversity. 

Land managers and communities continue to be actively involved in protecting and restoring freshwater bodies and habitats of special value to them. 

The habitat of some freshwater species (for example, blue duck) is now severely restricted. Only a couple of complete river systems still lie within unmodified catchments and remain free of introduced species. 

There are over 770 lakes and innumerable ponds, covering around 3400 square kilometres. People have also created numerous lakes and ponds, and these, and some natural lakes, are managed for a variety of purposes including water supply and power generation. Their biodiversity values vary widely. The 30 or so large deep lakes are of generally high water quality and some support almost intact indigenous ecosystems. However, many of the around 700 shallow lakes are degraded by nutrient enrichment causing eutrophication - a few to the extent that they are incapable of sustaining fish life. Most of the fish communities are dominated by introduced species, and invasive exotic plant species are extensive in most lake systems. 

Wetlands represent some of New Zealand's most diverse ecosystems. However, swamps, bogs and marshes now cover only 1000 square kilometres, representing a loss of over 90 percent of the original area of wetland systems. There is great regional variation in the extent of loss, ranging from 63 percent in Southland to 99 percent in the Bay of Plenty. Of the remaining wetlands, many are degraded to varying extents by weed invasions, stock access, modifications to hydrological regimes, and barriers to fish migration. However, some of the remaining wetlands are large and have internationally significant biodiversity values, as do some remaining geothermal areas. 

As a result of pressures on freshwater habitats, and the effects of introduced species, pests and weeds and harvesting pressures, many freshwater species (particularly birds and insects) have a significantly restricted distribution. One third of the 29 identified species of indigenous freshwater fish is threatened.

There are still sizeable gaps in our knowledge of freshwater species (particularly in relation to algae and invertebrates) and of habitat requirements (including effects of riparian management). Public awareness, and to a lesser extent scientific effort, have been focused on the more obvious species, especially fish and birds. 

Current management 
Freshwater management is characterised by relatively complex and sometimes overlapping responsibilities for freshwater environments and species, under a large number of laws. Natural waters are vested in the Crown and managed and allocated by regional councils, while DoC, Land Information New Zealand (LINZ), regional councils and territorial authorities have various responsibilities for managing the beds of waterbodies and their surrounding land areas. Freshwater species are managed by DoC (most indigenous species), the Ministry of Fisheries (Mfish) (fish species for which there is some commercial harvesting), or fish and game councils (sports fish and game birds). 

Freshwater biodiversity issues are largely addressed within a broader water management context. A number of policy mechanisms are used or are being developed to manage freshwater resources. These include: RMA planning tools, such as district and regional plans; initiatives under the Sustainable Land Management Strategy and National Agenda for Sustainable Water Management (NASWM); the Environmental Performance Indicators programme; the 1986 New Zealand Wetlands Management Policy; the 1994 New Zealand Coastal Policy Statement; water conservation orders; conservation management strategies; and iwi management plans. 

Some waterbodies, principally lakes and wetlands, are partly protected within public conservation lands or on private land. Wetlands are now eligible for Nature Heritage Fund and Nga Whenua Rahui funding for protection. Very few rivers are protected for all or even most of their length, although eight water conservation orders (four more are pending) protect the waters of outstanding rivers or lakes. 

Managing freshwater habitats and ecosystems 
The threats to freshwater biodiversity are diverse and pervasive. Many land use practices adversely affect freshwater biodiversity, through their effects on freshwater habitats and ecosystems, including underground water systems. These practices include drainage, flood control schemes, removal of riparian vegetation, stock access and the addition of sediment, nutrients and contaminants from agricultural, forestry, industrial, residential and urban runoff. Management responsibilities and accountabilities are often not clearly specified in the freshwater environment. 

• Reduced flows in some rivers limit freshwater biodiversity, and therefore water allocation decisions - often seen primarily as an economic issue - may have significant biodiversity implications. 
• Barriers to fish migration in rivers can prevent fish from completing their life cycles; most indigenous fish species are diadromous (meaning that they migrate to and from the sea) and most catchments in New Zealand have some artificial barriers. For some species (such as eels) the effects of the barriers preventing downstream migration to spawning grounds may be the hardest to overcome. 
• Poor water quality in many rivers also frequently limits freshwater biodiversity, and therefore decisions about land use, as well as discharges to water, have significant implications for aquatic biodiversity. 
• The grazing and drainage of significant wetlands continue to reduce and degrade wetland habitats and ecosystems. Estuarine habitats - important to the life cycle of diadromous fish such as whitebait and some commercial fisheries such as snapper - are often most at risk from land use activities and coastal development. Indigenous freshwater biodiversity values have not yet been adequately incorporated into sustainable land management strategies and production sector strategies. 
• Possible sea level rise may also pose a threat to estuarine habitats and flood plain wetlands. 
• Geothermal ecosystems whose surface features are reserved may still be at risk from the effects of energy or fluid extraction through use of connected fields. 
• There are very few freshwater ecosystems remaining in their original or pristine state, and without active management these may be at risk of loss of indigenous biodiversity and as benchmarks to compare with more modified ecosystems. 
• Management of freshwater biodiversity presents special challenges because of the need to integrate land, water and fisheries management and to coordinate the use of a range of policy and management tools. The fragmented and overlapping responsibilities for management of freshwater ecosystems do not help effective coordination and integration, and accountabilities of agencies that share responsibility are often inadequately specified. The need for coordination also applies to the areas between freshwater and coastal environments. 
• The Crown's property and other interests in freshwater biodiversity are generally not well specified and in some instances are being challenged by iwi. 

• Information about protection priorities is deficient, but key areas known to be poorly represented include lowland lakes and rivers, floodplain wetlands, mid-altitude wetlands, and geothermal ecosystems. 
• The gap between land and freshwater environments in achieving representative protected areas suggests that a different approach is required in protecting freshwater ecosystems, with a special focus on the sympathetic management of freshwater and surrounding land areas. 
• Protecting freshwater biodiversity requires a high level of coordination between management agencies to ensure protection mechanisms are applied in a complementary and integrated way.

• Most freshwater ecosystems have been significantly modified by introduced species. 
• Many animal and plant pests are highly invasive in freshwater environments, but are not detected until the extent of their spread makes them difficult to control. 
• Effective technologies for control or eradication of known pests (for example, koi carp) are not always available. 
• Policies, responsibilities and accountabilities for containing the spread of already established introduced freshwater species that have the potential to become serious pests are not fully developed. 
• The illegal transfer and release of aquatic species create significant risks to indigenous freshwater biodiversity. 

Protection of indigenous freshwater species
Indigenous freshwater species are threatened from a variety of causes, including land use impacts and competition or predation from pest species. 

• Protection of threatened freshwater species depends largely on protection or restoration of their habitat, including the physical and biological characteristics of the habitat. 
• Our knowledge of the distribution and taxonomy of many indigenous freshwater species is limited. Existing survey and monitoring programmes are generally not sufficient to define freshwater biodiversity or to identify changes in freshwater species composition and abundance or habitat condition. 
• The effects of some introduced species on indigenous freshwater biodiversity are not fully understood. 
• We do not have sufficient knowledge about all freshwater species that are commercially harvested (for example, eels) to be confident that their harvest is sustainable in some areas. 
• Some rare or vulnerable freshwater species (such as giant and short-jawed kokopu fish) are harvested as part of otherwise sustainable whitebait fisheries. This can create difficulties in providing a secure status for such species and for protecting fragile populations from unnecessary harvest. 

• Recreational fishing for species such as trout, salmon or whitebait is highly valued by many New Zealanders (and overseas visitors). This creates a strong interest in the protection and restoration of freshwater habitat, but sometimes also creates a potential conflict between the protection of indigenous and introduced species.
• Maori cultural values with respect to water quality and interests in protecting freshwater ecosystems and habitats to enable the use of freshwater species generally complement objectives to conserve and sustainably use freshwater biodiversity (see Theme Seven).
• There is a generally low level of public understanding of the special characteristics, values and vulnerabilities of freshwater biodiversity (see Theme Eight). 

Action Plan

Objective 2.1 Protection and sustainable management of freshwater ecosystems²⁴ 

a) Ensure that management mechanisms, including mechanisms under the Resource Management Act and protected area statutes, adequately provide for the protection of freshwater biodiversity from adverse effects of activities on land and in water. 

b) Protect a full range of remaining natural freshwater ecosystems and habitats to conserve indigenous freshwater biodiversity, using a range of appropriate mechanisms. 

Key players: MfE*, DoC, MAF, LAs, LGNZ, iwi/hapu, primary production sector, NGOs25 

b) Develop and apply a comprehensive classification system for freshwater ecosystems, in line with the framework and criteria developed under the Environmental Performance Indicators Programme, to help identify protection priorities. 

Key players: MfE*, DoC, research providers, RCs, iwi/hapu 

c) Progressively protect priority representative freshwater habitats, using a suite of protective mechanisms. 

Key players: DoC*, MfE, LGNZ, RCs, QEII Trust, Landcare Trust, F&GNZ, NGOs, iwi/hapu 

d) Review the range of available protective mechanisms for freshwater biodiversity and determine any required changes to improve their efficiency and effectiveness, including the removal of disincentives to protection. 

Key players: DoC*, MfE, LAs, iwi/hapu, primary production sector, land managers, community groups, QEII Trust 

e) Support, and where necessary develop, joint national and regional/local incentive mechanisms for protecting scarce and under-represented freshwater bodies and their surrounding areas on private land, and provide support to landowners to maintain the biodiversity values of these areas (see Action 1.1f). 

Key players: DoC*, MfE, LAs, iwi/hapu, primary production sector, land managers, community groups, QEII Trust 

f) Provide advice and support to land managers and communities (both rural and urban) who wish to protect freshwater waterways, wetlands and habitats in their area to encourage the protection of areas that are a priority for indigenous freshwater biodiversity. 

Key players: DoC*, MfE, LAs, iwi/hapu, primary production sector, land managers, community groups, QEII 

g) Develop clear national criteria for protecting and managing biodiversity in wetlands and geothermal systems through a review of the 1986 Wetlands Policy and 1986 Geothermal Policy, and incorporate in a national policy statement on biodiversity (see Action 1.1d). 

Key players: DoC*, MfE*, RCs, F&GNZ, MoC, iwi/hapu, NGOs 

h) Expand monitoring procedures (and establish new ones) for freshwater bodies (including lakes, rivers, underground systems, wetlands and geothermal systems) important for indigenous biodiversity to enable early action to maintain these ecosystems. 

Key players: DoC*, MfE, research providers, RCs, iwi/hapu 

Prevent, control and manage plant and animal pests that pose a threat to indigenous freshwater biodiversity.

Key players: DoC*, RCs*, Biosecurity Council, MAF, iwi/hapu, research providers 

Restore areas of degraded or scarce natural freshwater habitat and ecosystems that are priorities for indigenous biodiversity. 

Key players: DoC*, MfE*, LAs, iwi/hapu, F&GNZ, NGOs 

b) Compile regional inventories of significant artificial barriers to the migration to and from the ocean of indigenous freshwater species and progress priority actions to restore fish passage. 

Key players: DoC*, RCs, F&GNZ, iwi/hapu 

Enhance population numbers and ranges of indigenous freshwater species threatened with extinction and prevent additional species and ecological communities from becoming threatened. 

Key players: DoC*, NGOs, research providers, iwi/hapu 

b) Increase and implement planned recovery actions to cover priority threatened freshwater species so that viable representative populations are maintained or restored across their natural range. 

Key players: DoC*, research providers, LAs, NGOs, iwi/hapu 

Ensure that harvest of indigenous and introduced freshwater species and associated activities do not adversely affect indigenous freshwater biodiversity.

Key players: DoC*, Mfish, F&GNZ, NGOs, iwi/hapu

²³ Actions shown in bold are priority actions (see Part Four). 

²⁴ Objectives 2.1a and b are interrelated and actions a) - h) will collectively contribute to their achievement. 

²⁵ See key to key players. 

*Government lead