Seasonal variations in vertical density structure, inorganic nutrient concentrations, dissolved oxygen concentrations, and phytoplankton biomass were investigated in a shallow, tidally choked coastal lagoon subject to impaired water quality. Vertical turbulent mixing rates, which govern the distribution of scalars relevant to water quality, were quantified on both seasonal and diurnal time scales. The project site, Rodeo Lagoon, is located in the Golden Gate National Recreation Area, California, and has experienced fish kills and intense algae blooms in recent years.

Monthly measurements collected along a transect of the lagoon from March 2006 to April 2008 show it was strongly stratified by brackish water in winter, when freshwater inputs from the watershed and saltwater inputs from storm surge were both at their largest. The squared buoyancy frequency exceeded 0.5 s^-2 under these conditions, and the lower layer was typically warmer, depleted in oxygen and enriched in ammonium. In summer, weaker diurnal temperature stratification was the result of strong light absorption in this hypereutrophic lagoon. In fall 2007, hypoxia and potentially toxic levels of ammonium were observed coincident with the seasonal decline in algal biomass.

Wind is the dominant driver of turbulent mixing in Rodeo Lagoon. Although water depths of less than 2.5 m lead to the expectation of rapid vertical mixing, limited fetch and strong density gradients reduce the coupling of wind stress and bottom stress. The vertical turbulent diffusivity is reduced by as much as three orders of magnitude across the pycnocline, and the water column in and below the pycnocline shows active turbulence only intermittently. The annual cycle of salt-based stratification and accompanying reduction in turbulent exchange of nutrients between the sediments and overlying water column inhibit the flushing of nutrients out of the lagoon and contribute to excessive phytoplankton biomass.