Sea level rise (SLR) driven by climate change is widely recognized as a key factor contributing to increased saltwater intrusion (SWI) in coastal aquifers. However, the extent of SWI caused by SLR depends on how inland freshwater boundary conditions are defined. Previous studies have demonstrated that models utilizing head-controlled (HC) freshwater boundary conditions predict significant additional SWI, while those employing flux-controlled (FC) boundary conditions suggest negligible additional intrusion. Despite these contrasting outcomes, the broader hydrological effects of inland boundary conditions on coastal water balance have not been thoroughly investigated. In this study, we apply a well-established field-scale conceptual model to systematically analyze the hydrological implications of different inland freshwater boundary conditions in coastal aquifers experiencing SLR. Our findings indicate that coastal aquifers respond differently depending on boundary conditions: i) under HC conditions, aquifers exhibit a flux-decline effect, where freshwater fluxes, including submarine groundwater discharge, decrease over time, and ii) under FC conditions, aquifers experience a head-lift effect, where freshwater heads rise in response to SLR. Additionally, our results reveal that HC aquifers undergo prolonged transients in salt wedge movement, indicating a delayed response to historical sea-level changes. The flux-decline effect in HC systems alters the overall coastal hydrological balance of both aquifers and catchments, necessitating comprehensive hydrological assessments to accurately evaluate freshwater availability. Conversely, FC systems maintain mass balance and do not experience hydrological water balance alterations. However, the head-lift effect in FC aquifers can contribute to surface inundation in low-lying regions with topographic limitations. Our study enhances the understanding of SWI mechanisms and highlights the hydrological consequences of inland boundary conditions when assessing the impacts of SLR on coastal aquifers and freshwater sustainability.