In addition to a loss of potential revenues from Utah's $393 million sport fishing industry, the state expends millions of dollars every year on costs associated with whirling disease mitigation and prevention. A state fish hatchery at Midway, Utah was closed when the shallow unconfined aquifer being used for fish culture by spring discharge was deemed to be contaminated by whirling disease. An alternative water source may exist in a confined aquifer below this contaminated unconfined aquifer. However, the complex hydrostratigraphy presents a challenge in determining if this source is a viable resource for fish culture. Geological, physical, chemical, geophysical, and isotopic data were combined to create a conceptual model of the groundwater flow at the site and to determine the interactions this confined aquifer may have with the contaminated aquifer. This model divides groundwater at the hatchery into a shallow unconfined system, an upper confined system, and a lower confined system. The shallow unconfined system is characterized by a water table ~1m below ground surface, several active springs, fast travel times, modern water mixed with ancient hydrothermal water, relatively high TDS, and relatively enriched isotopic values. The confined aquifers have a smaller hydrothermal component, relatively depleted isotopic values, lower TDS, and modern recharge components. Two orthogonal shallow high-resolution seismic reflection profiles indicate substantial heterogeneity in the subsurface at the level of the confined systems at the hatchery. Several north-south trending normal discontinuities were interpreted as possible faults from the seismic profile oriented as a dip line, whereas the strike profile shows discontinuous layering without noticeable faulting. A well log profile for the site shows discontinuous tufa layers amid heterogeneous alluvium material. These tufa layers separate upward leaking confined aquifers from the unconfined system. It is only through the integration of several methods that such mixed systems, can be understood. In this study, the lower confined aquifer was found to be a sufficient and safe resource through the integration of numerous methods.