Lindane and naphthalene were used in a series of flow-through microcosms to validate predictions of two environmental fate models—the exposure analysis modeling system (EXAMS) and simplified lake and stream analysis (SLSA). The microcosms' physical transport characteristics were carefully measured and used as input parameters to the models, along with laboratory data on lindane and naphthalene rate constants and coefficients. The results show that both models accurately predict the chemicals' concentrations in the water compartment. Observed concentrations in the sediments were two to three orders of magnitude lower than the models' predictions, even though the overall mass balance accounted for about 90% of the chemicals' input. Lack of agreement between observed and predicted sediment concentrations may be attributed to (a) the variability of the sediment partition coefficient values, (b) the slow rate of sediment loading, (c) vertical stratification of the chemicals in the sediment, and (d) microbial degradation of the chemicals in the sediment.