Experience with groundwater remediation over several decades has demonstrated that successful outcomes depend on quantitative conceptual site models (CSMs). Over the last 30 years, we have progressed from groundwater pump‐and‐treat remedies, which were largely designed based on a water supply perspective, to in situ and combined remedy strategies, which are only beginning to benefit from understanding the aquifer architecture and distribution of contaminant mass to assess plume maturity, mass flux, and more reliable means of fate and transport assessment. The U.S. Air Force funded the development of the Stratigraphic Flux approach to provide a framework for understanding contaminant transport pathways at its complex sites and enable more reliable and cost‐effective remediation. Stratigraphic Flux enables the development of quantitative, flux‐based CSMs that are founded in sequence stratigraphy, and high‐resolution hydraulic conductivity and contaminant distribution measurements. The result is a three‐dimensional graphical mapping of relative contaminant flux and classification of transport potential that is easy for all stakeholders to understand. The Stratigraphic Flux graphical model is based on a hydrofacies classification system that describes transport potential in three segments of the aquifer: transport zones—where the majority of groundwater flow occurs and transport rates are measured in feet per day; slow advection zones—where transport rates are measured in feet per year; and storage zones—where typically less than 1% of flow occurs, and diffusion dominates contaminant transport. The hydrofacies architectures are based on stratigraphy and transport potential is defined by grouping facies by orders of magnitude classes in hydraulic conductivity. By combining the hydrofacies architecture with contaminant concentration distributions, one can map relative contaminant flux to define and target the complex pathways that control contaminant transport and cleanup behavior. In this article, we describe the Stratigraphic Flux framework, focusing on the key information needed and the methods of analysis. We illustrate the results of its application to evaluate migration pathways for trichlorethylene and chromium at a former chrome pit at Air Force Plant 4 in Fort Worth, Texas. A comprehensive guidance document that describes the approach with a broad spectrum of tools and several site examples can be requested from the authors.