This screening modeling analysis examines mercury sources and fate in the upper canals of the South Florida Everglades. Mass balance modeling techniques are applied along with available data to examine the relative importance of external sources and internal cycling of mercury and the relative influence of several transport and transformation processes. WASP5, a general dynamic mass balance model for aquatic systems, was modified to represent elemental mercury, divalent mercury, and methyl mercury. A new soil mercury mass balance model was developed to track the transport of these mercury components from soil surfaces to the water via surface runoff. Subsurface flow (drainage) loads were estimated on a seasonal basis using information from a modified simulation model for muck soil hydraulics and transport. Predicted mercury concentrations in the Everglades Agricultural Area (EAA) canals were compared to observed data provided by a region‐wide statistical sampling program. The modeling system reproduced the average mercury dynamics observed in the EAA canals during four surveys within a 2‐year period. Results indicate that despite the complexity of the upper South Florida Everglades ecosystem, the modeling system provides a plausible description of the average mercury dynamics in the EAA canals. Mercury concentrations in the canals appear to be dominated by runoff loading events from the EAA during the wet season, and by subsurface flow (drainage) loading between events and during the dry season. Predicted mercury concentrations in water leaving the EAA are similar to or slightly less than average concentrations in downstream marsh environments for most of the year. Predicted concentrations following large rainfall events, however, are significantly higherthan concentrations in the downstream marsh. These results must be considered as tentative due to the screening‐level character of the modeling study. They point to more detailed field monitoring and process studies which could confirm these findings.