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Environmental tracer or pollution patterns in groundwater have been regarded as a qualitative means of studying complex or large-scale hydrogeologic systems. However, questions have arisen as to whether the “natural state” analog has quantitative value, such as for the estimation of transport or aquifer parameters. In this paper we demonstrate the application of spectral analysis and frequency domain methods to temporal tracer patterns for the physical interpretation of transient environmental tracers in a variety of hydrologic settings. Three case studies are examined where the source of environmental tracer is represented as a stochastic process. Process and parameter estimation is performed by comparison of the theoretical transfer function and phase spectrum. The most important result of this paper is that different source configurations (nonpoint, point, etc.) and different groundwater flow patterns produce unique frequency response characteristics for solutes within each system. It is this feature which allows us to make inference about the governing physical processes and parameters.