Salt intrusions can exist within rivers and are influenced by shape of an estuary and tidal and river flows. Incoming tidal water moves into a region of freshwater influence which can have a strong influence on biological and geochemical properties in the water column. These features constitute a transition zone with spatially and temporally varying dynamics. As such, it is challenging to correctly represent these features in numerical hydrodynamic and sediment transport models. We report field observations of the salt intrusion processes in the Waihou River estuary in New Zealand. Most of the research that has been conducted thus far on the Waihou River has centred around sediment transport, gold mining impacts, water quality and fish populations and there is a lack of systematic collection of vertical water property data. Measurements of water column properties (salinity, temperature and turbidity) were taken at different tidal stages and river flows and used to track the movement and characteristics of the salt intrusion. In-situ water samples were collected and used to form a calibration for suspended sediment concentrations. The salinity intrusion was observed to intrude to 7.2-11.8 km (at 1 PSU) upstream from the mouth of the river. The estuary exhibited both mixed and stratified conditions, with a clear salt wedge shape observed for only one out of five surveys. The salinity intrusion length appeared to be primarily controlled by the by river flow, with a shorter intrusion length and stronger stratification occurring for higher river flows. Greater turbidity was observed within the marine water compared to fluvial waters, and turbidity was greater near the bed implying that the primary delivery mechanism of sediment to the lower reaches of the river is import from the offshore or intertidal marine regions. Numerical hydrodynamic modelling using Delft 3D was undertaken and was compared to the field data. While the model had previously been calibrated for water levels and velocity in two-dimensions, the adapted 3D version of the model did not accurately predict the structure or extent of the salinity intrusion. Model results under-estimated the salinity intrusion, which was attributed to over-mixing of the water column, however, the performance improved when a lower value for horizontal eddy diffusivity was used. This work emphasises the need to obtain vertically resolved data sets to allow for robust calibration of numerical models, which are commonly used in environmental management decisions.