Kristen A. Davis

Dissolved oxygen (DO) is a critically important ecological variable, and the prevalence of marine hypoxia is expected to increase due to the combined effects of ocean warming and eutrophication. Thermal stress can co‐occur with hypoxia, especially in tropical systems, and can exacerbate its effects. We examine the physical processes that are important in regulating hypoxia and temperature inversions in Bahía Almirante, a semi‐enclosed tropical embayment on the Caribbean coast of Panama. A 10‐yr record of observations at 7 locations within Bahía Almirante reveals seasonal temperature inversions and hypoxia at depth that often co‐occur. These features are more severe and persistent in the back bay, though they occur throughout Bahía Almirante. DO reductions correspond to periods with high freshwater input, including direct precipitation, resulting in strong salinity stratification that isolates bottom waters, allowing biological oxygen demand to draw down DO. Evidence indicates that lateral advection can contribute to reoxygenation events, and the relationship between near bottom DO and bottom salinities in the mid bay and back bay is consistent with deep‐water renewal as the mechanism for bottom water ventilation. These hypoxia and temperature inversion events impact the biological communities of Bahía Almirante, and the physical dynamics that regulate these coincident and persistent stressors for marine organisms are likely present in other shallow, tropical estuaries.

Idealized numerical modeling of thermally driven baroclinic exchange is performed to understand how cross‐shore flow is modulated by steady alongshore currents and associated shear‐generated turbulence. In general, we find that shear‐driven vertical mixing reduces the temperature gradients responsible for establishing the baroclinic flow, such that cross‐shore thermal exchange diminishes with alongshore current speed. Circulation in a base‐case simulation of thermal exchange with no alongshore forcing contains a cooling response consisting of a midday flow in the form of a downslope current with a compensating onshore near‐surface flow driving cross‐shore exchange, followed by an afternoon warming response flow via an offshore‐directed surface warm front, with a compensating return flow at the bottom. Nighttime convective cooling enhances vertical mixing and decelerates the warming response, and the diurnal cycle is renewed. In this base‐case scenario, representative of tropical reef environments with optically clear water and weak alongshore flow, surface heating and cooling can drive cross‐shore circulation with O (1) cm s −1 velocities. Alongshore flow forcing is implemented to induce upwelling‐ and downwelling‐favorable cross‐shore circulation. For mild alongshore forcing, the baroclinic cross‐shore exchange flow is enhanced due to an increase in the horizontal temperature gradient. Stronger alongshore flow leads to diminished thermally driven exchange, ultimately reaching a regime where the cross‐shore exchange is due predominantly to Ekman dynamics. Though exchange velocities are relatively small ( O (1) cm s −1 ), these persistent exchange flows are capable of flushing the nearshore region multiple times per day, with important implications for water properties of nearshore ecosystems.