Atrazine is a commonly used agricultural herbicide that is prone to leaching and exceeds the E.P.A. Maximum Contaminant Level in aquifers of several states. Molecular simulations can provide objective, energy-based models for the atomic-scale structural relationships among clay surfaces, cations, water, and organics in smectite interlayers. We performed molecular dynamics simulations of atrazine in the interlayers of three model smectites (a saponite and Wyoming and Arizona montmorillonites), each containing one, two, and three layers of interlayer water. In smectites containing a monolayer of interlayer water, atrazine necessarily oriented parallel to the basal surfaces and interacted directly (no intervening water molecules) and simultaneously with both opposing basal surfaces. The negatively charged ring-N and -Cl atoms of atrazine interacted with multiple interlayer ions in both inner- and outer-sphere complexes, while most of the atrazine molecule occupied more-hydrophobic surface sites between charge sites in the smectite layers. For more expanded smectites with two or three layers of interlayer water molecules, fewer atrazine-cation complexes formed, and the atrazine typically inclined at an acute angle relative to the basal surfaces. The two alkyl side chains tended to interact directly with one basal surface each. The rest of the atrazine molecule was forced to interact with interlayer water molecules. These simulations help rationalize experimental adsorption isotherm data and also present several hypotheses for future spectroscopic investigation of atrazine-smectite systems.