|The Whangamarino wetland is internationally recognised and one of the most important lowland wetland ecosystems in the Waikato Region. The wetland’s hydrology has been altered by reduced river base levels, the installation of a weir to raise minimum water levels and the Lower Waikato Waipa Flood Control Scheme, which is linked via the (hypertrophic) Lake Waikare and affected by varying catchment land use practices. When water levels exceed capacity, the overflow is released into the Whangamarino wetland, which also receives flood waters from Whangamarino River. Water levels in the wetland are also affected at high stage, by a control structure near Meremere at the confluence of Waikato and Whangamarino Rivers, and at low stage by a weir a short distance upstream. The ecohydrology of a representative part of the wetland was studied to assess the linkage between wetland ecology and the natural and anthropogenic modification of the flood regime and land use. The primary goal of this research was to characterise the present state of the wetland, which will aid in developing future goals and approaches for restoration. The study focused on a 2.3 km transect extending from the Whangamarino River, through the wetland to adjacent farmed hillsides. Hydrological and meteorological data were retrieved and analysed from an automated weather station and seven water level sites along the transect. Historical water level records (over 46 years) were used to determine changes in the hydrological regime and the impact of the flood control scheme, through a flood inundation and frequency analysis. During a winter flood event, river water quality was assessed. Peat surface oscillation in the restiad bog was examined. Vegetation patterns were assessed and classified through ordination and statistical techniques. Peat, soil and foliage physical and chemical quality were measured. Atmospheric ammonia (NH3) deposition rates of N into the wetland were measured. Water levels in the inland 0–1.1 km of the transect line (restiad bog) were relatively stable and consistent, rising and falling through winter and summer. This area had rainfall as the primary water input and was independent from the Whangamarino River, except during large flood events where the fringe of the restiad bog was inundated. Closer to the Whangamarino River water levels were more variable and strongly responsive to the river’s hydrological regime. A flood inundation event in September 2010 impacted on wetland water level regimes up to 1.4 km from the river and had a return period of 3.3 years. Frequency analysis showed sites up to 500 m from the river will likely be inundated by floods every year. A 100 year flood was estimated to inundate 1.75 km from the river, but would not cover the entire wetland. River water samples collected during a flood event showed total suspended solids within the Whangamarino River peaking at 260 mg L-1, double the concentration from Pungarehu Canal (86 mg L-1). Nutrient concentrations (such as dissolved reactive phosphorus) followed a similar pattern to the flood hydrograph. Minimum water levels have increased since the development of the artificial weir, but before this occurred water table lowering may have encouraged manuka invasion towards the restiad bog. Increased flood inundation is now the most likely threat to continued wetland degradation and manuka invasion into the restiad bog, due to the change in water levels and the deposition of sediment and nutrients. Nutrients, heavy metals, isotopes (δ15N) and physical soil characteristics (such as bulk density) increased from the start of the manuka belt (1100 m) and were greatest near the Whangamarino River (2300 m). A gradient was observed in peat and soil chemistry patterns, with increasing fertility and a change from bog to swamp-type environments along the transect line towards the river. A mineralised swamp fringe belt was present next to the farmland (0–50 m). From 50–1100 m a restiad bog (dominated by Empodisma minus) was present and changed to a manuka transition zone from 1100–1500 m. From 1500–1900 m, a swamp environment was present with a dominant canopy of manuka changing to Coprosma tenuicaulis closer to the river. C. tenuicaulis appears to be acting as a buffer zone over 150 m, removing a large amount of nutrients and sediment from flood waters. The remaining 400 m (1900–2300 m) of the transect line was a marshland, with the highest nutrient and sediment abundances and the most variable water level patterns. This area was colonised primarily by Polygonum persicaria (willow weed). The major risk to the wetland is from continued flood inundation with nutrient and sediment rich waters. Recommendations for future management include restoring catchment water quality and better management of the flood control regime.