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A new method was developed for conducting aquifer tests in fractured-rock flow systems that have a pump-and-treat (P&T) operation for containing and removing groundwater contaminants. The method involves temporary shutdown of individual pumps in wells of the P&T system. Conducting aquifer tests in this manner has several advantages, including (1) no additional contaminated water is withdrawn, and (2) hydraulic containment of contaminants remains largely intact because pumping continues at most wells. The well-shutdown test method was applied at the former Naval Air Warfare Center (NAWC), West Trenton, New Jersey, where a P&T operation is designed to contain and remove trichloroethene and its daughter products in the dipping fractured sedimentary rocks underlying the site. The detailed site-scale subsurface geologic stratigraphy, a three-dimensional MODFLOW model, and inverse methods in UCODE_2005 were used to analyze the shutdown tests. In the model, a deterministic method was used for representing the highly heterogeneous hydraulic conductivity distribution and simulations were conducted using an equivalent porous media method. This approach was very successful for simulating the shutdown tests, contrary to a common perception that flow in fractured rocks must be simulated using a stochastic or discrete fracture representation of heterogeneity. Use of inverse methods to simultaneously calibrate the model to the multiple shutdown tests was integral to the effectiveness of the approach.