This paper provides a model approach for understanding mercury cycling in aquatic systems. The information gained is then used for evaluating three remedial actions, namely, natural attenuation, dredging and capping. Onondaga Lake, NY was used as a model aquatic system. Mercury transport and speciation in both the water column and the benthic sediment were simulated by using a Water Quality Analysis Simulation Program. Model predictions for the water column generally agreed with the measured values reported in literature for Onondaga Lake. Sensitivity analyses of the model were conducted for determining the impact of transport mechanisms and speciation mechanisms. Advection, sorption and settling were important mechanisms of Hg transport in the water column. In the benthic sediment, settling of Hg from the water column was the most important input source of Hg. Reduction, methylation and demethylation were important mechanisms of Hg speciation in both the water column and the benthic sediment. Assuming that Hg loading is steady, natural attenuation showed no positive impact for remediation of Hg-contaminated aquatic systems as compared with dredging and capping.