<p>Climate change-induced sea level rise (SLR) is widely perceived as a significant driver of increased saltwater intrusion (SWI) in coastal aquifers. Previous studies show that, depending on the choice of inland freshwater boundary conditions, models predict contrasting results regarding SWI due to SLR. While simulations employing head-controlled (HC) freshwater boundary conditions show considerable additional SWI, those using flux-controlled (FC) freshwater boundary conditions show negligible additional SWI. However, the hydrological implications of inland freshwater boundary conditions on coastal water balances remain underexplored. Here, a widely studied field-scale conceptual problem is employed to comprehensively assess the hydrological implications of inland freshwater boundary conditions in coastal aquifers subject to SLR. The results show that coastal aquifers subject to SLR under: (i) HC conditions experience a flux-decline effect wherein freshwater fluxes reduce; and (ii) FC conditions experience a head-lift effect wherein freshwater heads increase. The analysis shows that HC aquifers exhibit prolonged transient responses in salt-wedge movement, suggesting ongoing responses to recent sea level changes. Additionally, the flux-decline effect in HC systems alters the overall aquifer and catchment coastal hydrological water balances and requires appropriate hydrological evaluations. FC systems, on the other hand, are mass-conservative and do not suffer from hydrological water balance artifacts. However, the head-lift effect in FC aquifers can cause inundation in low-lying regions with topographically limited aquifers. This study helps to comprehensively characterize the underlying mechanisms behind SWI and the hydrological implications of the choice of inland boundary conditions for studying the impacts of SLR.</p>