Chemical transport plays a key role in naturally heterogeneous geological media, across scales from rock pores to aquifers. While it is common to expect that “the shortest path between two points is a straight line”, this is, invariably, not the case for water and chemical transport in soils and aquifers. Indeed, complex flow pathways often result in surprisingly fast, early-time arrivals of pollutants, as well as anomalously (and often annoyingly!) long-time delays. When chemicals are reactive, groundwater systems can be altered by changes in solution chemistry and/or by a wide variety of chemical transformations; the latter include precipitation/dissolution reactions with feedbacks that directly affect the flow and transport regime. The combination of chemical reactions with advective/dispersive/diffusive transport leads to a rich spectrum of complex dynamics. The principal challenge in modeling chemical transport is to account for the subtle effects of fluctuations in the flow field and species concentrations; critically, spatial or temporal averaging suppresses these effects. Moreover, it is critical to ground model conceptualizations and test model outputs against laboratory experiments and field measurements. We focus on the integration of these aspects, considering case studies in different frameworks.