Density stratification in saline and hypersaline water bodies from throughout the world can have large impacts on the internal cycling and loading of salinity, nutrients, and trace elements. High temporal resolution hydroacoustic and physical/chemical data were collected at two sites in Great Salt Lake (GSL), a saline lake in the western USA, to understand how density stratification may influence salinity and mercury (Hg) distributions. The first study site was in a causeway breach where saline water from GSL exchanges with less saline water from a flow restricted bay. Near-surface-specific conductance values measured in water at the breach displayed a good relationship with both flow and wind direction. No diurnal variations in the concentration of dissolved (<0.45 μm) methylmercury (MeHg) were observed during the 24-h sampling period; however, the highest proportion of particulate Hgtotal and MeHg loadings was observed during periods of elevated salinity. The second study site was located on the bottom of GSL where movement of a high-salinity water layer, referred to as the deep brine layer (DBL), is restricted to a naturally occurring 1.5-km-wide “spillway” structure. During selected time periods in April/May, 2012, wind-induced flow reversals in a railroad causeway breach, separating Gunnison and Gilbert Bays, were coupled with high-velocity flow pulses (up to 55 cm/s) in the DBL at the spillway site. These flow pulses were likely driven by a pressure response of highly saline water from Gunnison Bay flowing into the north basin of Gilbert Bay. Short-term flow reversal events measured at the railroad causeway breach have the ability to move measurable amounts of salt and Hg from Gunnison Bay into the DBL. Future disturbance to the steady state conditions currently imposed by the railroad causeway infrastructure could result in changes to the existing chemical balance between Gunnison and Gilbert Bays. Monitoring instruments were installed at six additional sites in the DBL during October 2012 to assess impacts from any future modifications to the railroad causeway.