The University of Waikato was contracted by Waikato Regional Council to develop a hydrodynamic model of the Waikato River delta to aid with the assessment of whitebait spawning habitat, and to help inform restoration plans for the area. The Waikato River estuary and delta cover the lowest reaches of the Waikato River, less than c. 15 km from the sea. The estuary is classed as a tidal river mouth and is mostly subtidal, whilst the delta is the widest part of the river and estuary and extends from 6 to 15 km from the entrance. The most common whitebait species in the lower Waikato River is juvenile īnanga, Galaxias maculatus, a diadromous fish species that matures in freshwater and then migrates downstream to spawn in a tidal estuary. īnanga spawn close to the interface between fresh and saltwater, in bankside vegetation that is inundated only on spring tides, and spawning sites in the lower Waikato River have mostly been found in and around the delta. As there have been few published studies on the physical or ecological characteristics of the Waikato River estuary or delta, there is currently limited understanding of the impact of tidal state and river flow on salinity distributions and water levels, which will likely exert significant influence on the location of īnanga spawning sites. Whilst collating available data it was found that there was limited bathymetry, and little data on water levels, temperature and salinity in the estuary and delta. These data are required for the calibration and validation of hydrodynamic models of water transport and mixing. To address this paucity of data a field survey (measuring spatial and temporal variability in parameters such as temperature and salinity) was conducted by the University of Waikato, and Waikato Regional Council contracted Discovery Marine Ltd to conduct a hydrographic survey of the estuary and delta region. Bathymetry data from the hydrographic survey was used in hydrodynamic modelling of the estuary and delta, and GIS modelling of potential floodplain inundation. This report details the results of the field survey and GIS modelling, as well as the hydrodynamic model simulations, as these studies provide significant insight into spatial and temporal variability in ecologically relevant parameters and potential whitebait spawning habitat. A field survey was conducted in the Waikato River estuary and delta over a spring-neap tidal cycle in April 2013. Data loggers measuring water level, temperature, conductivity, and other water quality parameters, such as dissolved oxygen and turbidity, were deployed at several locations in the estuary and delta over a 16-day period. In addition, boat surveys used a Conductivity-Temperature-Depth (CTD) probe and a towed horizontal profiler to map spatial variability in temperature and conductivity, and to determine the extent of saltwater intrusion into the estuary under neap tide and spring tide conditions. The surveys indicated that there was considerable variability in temperature and salinity distributions in the estuary and delta, both laterally and longitudinally. In contrast, there was little vertical variation, as the water column was typically well-mixed, except in the very lowest reaches of the estuary where a distinct salt wedge was sometimes observed. The limit of saltwater intrusion into the estuary and delta was found to be in the mid-islands region, c. 10 km from the entrance, on the neap tide survey and in the upper islands, c. 13 km from the entrance, on the spring tide survey, which is further than has previously been reported. Water level loggers revealed marked tidal asymmetry at sites upstream of the entrance, caused by bottom friction and the interaction of the tidal wave with freshwater discharge. There was substantial temporal variability in variables such as temperature, salinity and dissolved oxygen, related to diurnal and tidal cycles, and river flow, and these also provided critical data that was then used in calibration and validation of the hydrodynamic model.