Marine sensitive clay deposits along the St. Lawrence and Saguenay–Lac St-Jean Lowlands in Québec are traditionally considered to be unfractured below a shallow weathered crust. Using cross-correlation analysis of hydraulic head data from a dense network of vibrating-wire piezometers, this study demonstrates the presence of hydraulically active fractures extending to depths of up to 16 m. These fractures significantly alter the prevailing conceptual model of groundwater flow in clay-rich environments by including rapid recharge and discharge processes that were previously assumed to be strongly attenuated due to low matrix permeability. To assess the implications of these fractures, transient and steady-state groundwater flow models were developed with and without fracture networks, and applied to slope geometries exhibiting contrasting flow directions. Results show that fractures can either enhance infiltration and increase hydraulic head, or accelerate discharge and reduce hydraulic head along slope faces. This dual behavior highlights the complex role of fractures in shaping groundwater flow systems, recharge–discharge interactions, and slope stability in sensitive clays. From a hydrogeological perspective, fractures represent critical pathways that may strengthen or weaken slope stability depending on the prevailing groundwater system. Beyond geotechnical concerns, these findings underscore the importance of considering fracture-mediated recharge and discharge in sensitive clay deposits when evaluating groundwater dynamics, ecosystem resilience, and surface water–groundwater interactions.