The Indian River Lagoon (IRL), a micro-tidal subtropical estuary on the east coast of central Florida, is strongly influenced by freshwater flows from a water shed defined by the Florida canal system. A clear understanding of the response of this estuary to strong and episodic inflows of freshwater is required to manage the impacts of these events on the estuarine ecosystem and associated habitats. Empirical orthogonal function (EOF) analysis was used to examine the relations among various temporally correlated hydrographic, hydrological, and meteorological parameters in the central IRL near the discharge point of a major canal. The results show that freshwater discharge dominates the hydrodynamic and mixing characteristics of the area of the lagoon that is directly affected by the discharge. The barotropic pressure gradient due to the lagoonward sloping of the river plume is the most important forcing and determines the flow field around the river mouth. Surface flow in the plume is driven toward the front that separates the plume from the ambient lagoon water. The horizontal density gradient between the distant part of the lagoon and the point of freshwater discharge is the second most important forcing, which drives a return flow in the denser layer beneath the surface plume. The episodic nature and the volume of the discharge determines the pulses of salinity stratification. The fourth important forcing is the wind, the most important external factor, which modified the direction and the extent of the river plume.