In recent years, there has been a growing recognition of the ecological significance of groundwater-dependent ecosystems (GDEs), which rely on groundwater for sustainability and face increasing vulnerability due to environmental stresses. This has led to a substantial body of literature investigating various aspects of GDEs and their hydrogeological connectivity to underlying aquifers. Nevertheless, the field lacks a comprehensive synthesis that integrates theoretical models, spatial data integration, and advanced groundwater modeling techniques. Furthermore, GDEs confront escalating threats arising from land-use changes, climate variability, and groundwater depletion, it becomes imperative to identify research gaps and limitations in current methodologies and approaches. This imperative guide the development of effective conservation and management strategies. Thus, this review offers a comprehensive exploration, delving into the background and classification of GDEs. It further examines a range of models and conceptual frameworks employed to understand the hydrogeological connectivity to underlying aquifers, while also assessing the integration of spatial data with numerical models for groundwater modelling. However, there are concerns with regards to the mismatch in spatial and temporal scales between remote sensing data and groundwater models, which leads to difficulties in integration. Furthermore, there is limited ground truth data, especially in remote areas, which further complicates validation efforts. However, this review identified the need for the integration of spatial data to groundwater numerical modelling to improve the accuracy of the model results by providing more detailed information about the geology and hydrogeology of the area being observed. Moreover, this review sheds light on the ecological significance of understanding GDE-aquifer connectivity and its critical role in conservation efforts within these ecosystems.