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Natural fissures/faults or pressure‐induced fractures in the caprock confining injected CO₂have been identified as a potential leakage pathways of far‐field native brine contaminating underground sources of drinking water. Developing models to simulate brine propagation through the overlaying formations and aquifers is essential to conduct reliable pre‐ and post‐risk assessments for site selection and operation, respectively. One of the primary challenges of performing such simulations is lack of adequate information about source conditions, such as hydro‐structural properties of caprock fracture/fault zone and the permeability field of the storage formation. This research investigates the impact of source condition uncertainties on the accuracy of leaking brine plume predictions. Prediction models should be able to simulate brine leakage and transport in complex multilayered geologic systems with interacting regional natural and leakage flows. As field datasets are not readily available for model testing and validation, three comprehensive intermediate‐scale laboratory experiments were used to generate high‐resolution spatiotemporal data on brine plume development under different leakage scenarios. Experimental data were used to validate a flow and transport model developed using existing code FEFLOW to simulate brine plume under varying source conditions. Spatial moment analysis was conducted to evaluate how uncertainty in source conditions impacts brine migration predictions. Results showed that inaccurately prescribing the permeability field of storage formation and caprock fractures in models can cause errors in leakage pathway and spread predictions up to ∼19% and ∼100%, respectively. These findings will help in selecting and characterizing storage sites by factoring in potential risks to shallow groundwater resources.