Numerical modeling of fluid flow and contaminant transport is often used to test hypotheses and to guide resource management. In complex natural systems, challenges are often associated with collecting sufficient information to parameterize numerical models over field relevant scales, and with the development of mathematical representations of critical, coupled hydrological-biogeochemical processes. Geophysical methods can be helpful for guiding or constraining numerical models because they can provide extensive information about subsurface properties and processes. Obtaining quantitative parameter estimates from geophysical approaches can also be challenging, however, as these methods do not sample hydrological-biogeochemical properties directly and are often sensitive to various influences. Through a series of lab and field-based case studies, we will explore the benefits and current limitations of using geophysical information in conjunction with hydrological models to interrogate natural systems. We illustrate that where geophysical characterization approaches are sufficiently advanced, they can be useful for guiding model development, providing model parameter input, and for exploring the impact of heterogeneity on flow and transport processes. We also illustrate that where characterization and modeling methods are less well developed, such as advanced subsurface reactive transport models or the use of geophysical methods for monitoring biogeochemical transformations, comparison of monitoring and modeling information can lead to improvements in the use of both methods as investigative tools.