Numerical simulators are frequently used to assess future risks, support remediation and monitoring program decisions, and assist in design of specific remedial actions with respect to groundwater contaminants. Due to the complexity of the subsurface environment and uncertainty in the models, many alternative simulations must be performed, each producing data that is typically postprocessed and analyzed before deciding on the next set of simulations. Though parts of the process are readily amenable to automation through scientific workflow tools, the larger "research workflow" is not supported by current tools. We present a detailed use case for subsurface modeling, describe the use case in terms of workflow structure, briefly summarize a prototype that seeks to facilitate the overall modeling process, and discuss the many challenges for building such a comprehensive environment.