Limestone aggregate quarries in deeply penetrating karst terrain are often at considerable risk of artesian inflow from groundwater or surface water channeled through the karstic aquifer. The inflow occurs through what are likely to be complex conduits that penetrate hundreds of feet into bedrock. Rates of inflow can exceed the operation's pumping capabilities proving to be uneconomic to manage over the long term. Over time, inflow rates can increase dramatically as turbulent flow through the conduit erodes its soft residual clay-rich fill. One recent investigation observed an inflow rate of more than 40,000 gpm from a surface water source. Floodwater persistently laden with sediment is an indicator of conduit washout and implies increasing inflow rates over time. Conduits carrying floodwater can exist in a variety of forms: along deeply penetrating geologic faults, joints, or following the path of preferentially eroded bedding. Preferential structural deformation along faults or bedding can enhance dissolution during subsequent interaction with groundwater. The resulting conduit may be a complex combination of many geological features, making the exploration and remediation of the pathway difficult. Sinkholes at the site can occur within several contexts. Pre-existing subsidence structures can reactivate and subside further, forming new collapse sinkholes within soil directly overlying the conduit. Cover-collapse sinkhole development can be a direct result of increasing downward groundwater velocities and subsurface erosion associated with the enlargement of a conduit. Normal operation events such as a quarry blast can also provide a significant new linkage between the groundwater and the quarry, allowing rapid drainage of the groundwater reservoir. With such drainage and erosion of karst-fill, sinkholes will develop over localized water table depressions, most significantly over enhanced permeability zones associated with fractures. Paradoxically, although the rise in quarry water level will lead to regional reduction in the hydraulic gradients, on local scales, drainage of the groundwater reservoir increases gradients and leads to the development of cover-collapse sinkholes. Recommended methods for preliminary site investigation can include a detailed review of geological literature and drilling logs to compile a conceptual model of the site. A fracture trace analysis with EM geophysics can confirm the locations of major faults and fractures. Fingerprinting of the various water sources to the quarry and the water in the quarry is an inexpensive and effective means of identifying the source and likely direction of the groundwater and surface water flow. Automated geophysical equipment on the market for performing rapid resistivity and microgravity surveys speeds up the site screening process during reconnaissance exploration for deep structure. It is recommended that mine planning fully incorporate this information so that quarry operators can take proactive measures to avoid catastrophic and costly flooding events.