Threats to New Zealand's remaining wetlands are mostly the result of human activities including:

 
Wetland in the Te Anau area

• Sand and gravel extraction causing changes in water level and access for weeds or damage to existing vegetation.
• Reclamation of lake and river margins, lagoons and estuaries and draining of farm swamps, reducing wetland areas.
• Excess run-off of sediment and nutrients which can pollute wetlands.
• Plant and animal pest invasion.
• Stock grazing in surrounding catchments and wetlands themselves. This damages vegetation, decreases soil stability and contributes to pollution.
• Loss of natural character, i.e. the natural appearance of wetlands in the landscape.
• Careless recreation practices including misuse of jet-skiing, hunting, kayaking, power boating and whitebaiting. Carelessness disturbs plant and animal life and may destroy parts of the physical wetland environment.
• Forest harvesting close to wetlands may damage wetland vegetation and cause erosion.
• Loss of vegetation in surrounding catchment which allows excess sediment to run directly into wetlands.
• Inappropriate use of surrounding land in a catchment, for example, pine forest drawing water away from ground water systems leaving depleted water supply, or poorly managed farming practices causing sediment and/or fertiliser run-off.
• Drainage of wetlands for urban or rural development.