The hydrodynamics of a coastal aquifer system was investigated in the Kendrapara district, Odisha, India. The analysis of 248 groundwater samples collected across one monsoonal season indicates that the anisotropic coastal aquifer is affected by salinity. Taking into account the hydrodynamic variables of hydraulic head, transmissivity, saturated thickness and the effective porosity of the aquifer, a Darcy flow analysis of groundwater was carried out to determine the flow volume residual, flow direction and flow rate of the aquifer system in the region. These modelled outputs display significant disturbed nature of groundwater ‘flow–regimes’ which, in turn, is suggestive of major structural changes to the depositional basin. Geospatial and geostatistical cluster analysis carried out for the modelled parameters in relation to the tectonic elements of the region indicated that faults have a significant influence on aquifer hydrodynamics and, in turn, on the hydrogeochemistry of the system. This inference is further justified from the spatial analysis of earthquake epicentres for the last 50 years which shows a close interrelationship with the ‘North Odisha Boundary Fault’. The investigation also draws inference from the sudden directional change of river Brahmani which seems to be affected by the ‘Mahakalapara–Rajnagar’ strike-slip fault. On the basis of these findings, it is suggested that the subsurface non-granular (clayey) horizons have been extensively deformed by the tectonic disturbances. This has led to the juxtaposition or detachment of aquifer domains which, in turn, has led to the intermixing of varied groundwater types giving rise to the observed salinity of the study region.