Deep basin aquifers are increasingly used in water‐stressed areas, though their potential for sustainable development is inhibited by overlying aquitards and limited recharge rates. Long open interval wells (LOIWs)—wells uncased through multiple hydrostratigraphic units—are present in many confined aquifer systems and can be an important mechanism for deep basin aquifers to receive flow across aquitards. LOIWs are a major control on flow in the deep Cambrian–Ordovician sandstone aquifers of the upper Midwest, USA, providing a source of artificial leakage from shallow bedrock aquifers and equilibrating head within the sandstone aquifers despite differential pumpage. Conceptualizing and quantifying this anthropogenic flow has long been a challenge for groundwater flow modellers, particularly on a regional scale. Synoptic measurements of active production wells and well completion data for northeast Illinois form the basis for a transient, head‐specified MODFLOW model that determines mass balance contributions to the region and estimates LOIW leakage to the aquifers. Using this insight, transient LOIW leakage was simulated using transiently changing KV zones in a traditional, Q‐specified MODFLOW‐USG model, a novel approach that allows the KV in a cell containing a LOIW to change transiently by use of the time‐variant materials (TVM) package. With this modification, we achieved a consistent calibration through time, averaging 19.9 m root mean squared error. This model indicates that artificial leakage via LOIWs contributed a minimum of 10–13% of total flow to the sandstone aquifers through the entire history of pumping, up to 50% of flow around 1930. Removal from storage exceeds 40% of flow during peak withdrawals, much of this flow sourced from units other than the primary sandstone aquifers via LOIWs. As such, understanding the timing and magnitude of LOIW leakage is essential for predicting future water availability in deep basin aquifers.