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The Mount Simon and Lower Knox Group Formations within the Illinois Basin, USA, are being considered as targets for carbon dioxide (CO $$_2$$ ) storage. Two main concerns related to the subsurface storage process are potential leakage of CO $$_2$$ from the storage formation to the atmosphere and possible migration of CO $$_2$$ or displaced brine into underground sources of drinking water. In this study we use a numerical model to represent the migration of both CO $$_2$$ and brine in the Mount Simon Sandstone and two overlying aquifers, the shallowest of which is considered a potential source of drinking water. A vertically-integrated approach is used to model the fluid flow, leading to a stack of two-dimensional subdomains which are connected by leakage through the aquitards which separate the aquifers. Each formation is discretized into 12,103 grid cells, each $$5 \times 5\,\mathrm{{km}}$$ , and permeability and porosity vary spatially. Two vertical refinements are used for the Mount Simon Sandstone: the first represents the Mount Simon as a single layer, while the second subdivides the formation into subunits within the formation that have varying petrophysical properties. The locations and injection rates of the hypothetical injection operations are based on existing sources of CO $$_2$$ associated with power generation, ethanol production, and oil and gas refineries. A total of 250.5 million metric tons are injected at 118 sites. The injection operations are assumed to continue for 50 years. Results indicate the maximum radial extent of the CO $$_2$$ plume increased from 40 to 50 km between the single layer and multi-layer representations of the Mount Simon. Maximum average pore pressures reached 8.6 MPa and the pressure envelop extended as much as 100 km from the injection wells with significant well-well pressure interference patterns. The maximum well head pressure exceeded the fracture pressure in some cases suggesting more wells may be needed at some of the lower permeability injection sites. Brine leakage into overlying shallower units was not significant. [ABSTRACT FROM AUTHOR]