High quality coastal aquifer systems provide vast quantities of potable groundwater for millions of people worldwide. Managing this setting has economic and environmental consequences. Specific knowledge of the dynamic relationship between fresh terrestrial groundwater discharging to the ocean and seawater intrusion is necessary. We present multi- disciplinary research that assesses the relationships between groundwater throughflow and seawater intrusion. This combines numerical simulation, geophysics, and analysis of more than 30 years of data from a seawater intrusion monitoring site. The monitoring wells are set in a shallow karstic aquifer system located along the southwest coast of Western Australia, where hundreds of gigalitres of fresh groundwater flow into the ocean annually. There is clear evidence for seawater intrusion along this coastal margin. We demonstrate how hydraulic anisotropy will impact on the landward extent of seawater for a given groundwater throughflow. Our examples show how the distance between the ocean and the seawater interface toe can shrink by over 100% after increasing the rotation angle of hydraulic conductivity anisotropy when compared to a homogeneous aquifer. We observe extreme variability in the properties of the shallow aquifer from ground penetrating radar, hand samples, and hydraulic parameters estimated from field measurements. This motived us to complete numerical experiments with sets of spatially correlated random hydraulic conductivity fields, representative of karstic aquifers. The hydraulic conductivity proximal to the zone of submarine groundwater discharge is shown to be significant in determining the overall geometry and landward extent of the seawater interface. Electrical resistivity imaging (ERI) data was acquired and assessed for its ability to recover the seawater interface. Imaging outcomes from field ERI data are compared with simulated ERI outcomes derived from transport modelling with a range of hydraulic conductivity distributions. This process allows for interpretation of the approximate geometry of the seawater interface, however recovery of an accurate resistivity distribution across the wedge and mixing zone remains challenging. We reveal extremes in groundwater velocity, particularly where fresh terrestrial groundwater discharges to the ocean, and across the seawater recirculation cell. An overarching conclusion is that conventional seawater intrusion monitoring wells may not be suitable to constrain numerical simulation of the seawater intrusion. Based on these lessons, we present future options for groundwater monitoring that are specifically designed to quantify the distribution of; (i) high vertical and horizontal pressure gradients, (ii) sharp variations in subsurface flow velocity, (iii) extremes in hydraulic properties, and (iv) rapid changes in groundwater chemistry. These extremes in parameter distribution are common in karstic aquifer systems at the transition from land to ocean. Our research provides new insights into the behaviour of groundwater in dynamic, densely populated, and ecologically sensitive coastal environments found worldwide.