The purpose of the present study was to evaluate the mercury (Hg) Environmental Ratios Multimedia Ecosystem Sources (HERMES) model on two Ontario, Canada lakes (Harp and Dickie) and to include modifications to enable the model to estimate the major model input variables that tend to be missing for lakes with limited datasets. No significant differences were found for either sediment solid or bulk water total mercury (THg) when the HERMES model was applied to the two Ontario lakes, regardless of whether all available data were altered during application or only the 10 variables that tend to cause the most variation in model output (i.e., concentration of THg in atmosphere, water inflow THg concentration, water inflow rate, water volume, surface area, mean depth, suspended particulate matter concentration, settling rate of solids in water column, water temperature, and precipitation rate). Since measured sediment and water THg values do not exist for most lakes removed from industrial activities, empirical relationships were incorporated into the HERMES model framework to provide a method to double-check model output for lakes where this information is unavailable.