The freshwater resources of coastal aquifers are vulnerable to seawater intrusion (SWI) caused by the current rising trends in sea levels, amongst other factors. Recent studies have examined the extents, rates and timescales associated with SWI induced by expected levels of sea-level rise (SLR), but have neglected the effects of transgression (i.e. inland migration of the shoreline in response to SLR). In this chapter, variable-density numerical modelling is used to examine the implications of transgression for a range of SWI scenarios based on simplified coastal aquifer settings. Vertical intrusion during transgressions can involve density-driven convective processes, causing substantially larger amounts of seawater to enter the aquifer and creating more extensive intrusion than that of horizontal SWI occurring in the absence of transgression. Interestingly, cases of transgression where no vertical mixing occurs involve reduced landward migration of the wedge toe, relative to otherwise similar situations without transgression. The rates and extents of SWI caused by transgression and associated vertical mixing appear to be almost non-responsive to the choice of landward boundary condition, contradictory to the findings of SLR-SWI studies that neglect transgression. The findings of this study suggest that modelling analyses that neglect the effects of transgression in SLR-SWI investigations may underestimate significantly the rates and extent of SWI.