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.

Land use and land cover (LULC) can significantly alter river water, which can in turn have important impacts on downstream coastal ecosystems by delivering nutrients that promote marine eutrophication and hypoxia. Well-documented in temperate systems, less is known about the way land cover relates to water quality in low-lying coastal zones in the tropics. Here we evaluate the catchment LULC and the physical and chemical characteristics of six rivers that contribute flow into a seasonally hypoxic tropical bay in Bocas del Toro, Panama. From July 2019 to March 2020, we routinely surveyed eight physical and chemical characteristics (temperature, specific conductivity, salinity, pH, dissolved oxygen (DO), nitrate and nitrite, ammonium, and phosphate). Our goals were to determine how these physical and chemical characteristics of the rivers reflect the LULC, to compare the water quality of the focal rivers to rivers across Panama, and to discuss the potential impacts of river discharge in the Bay. Overall, we found that the six focal rivers have significantly different river water characteristics that can be linked to catchment LULC and that water quality of rivers 10 s of kilometers apart could differ drastically. Two focal catchments dominated by pristine peat swamp vegetation in San San Pond Sak, showed characteristics typical of blackwater rivers, with low pH, dissolved oxygen, and nutrients. The remaining four catchments were largely mountainous with >50% forest cover. In these rivers, variation in nutrient concentrations were associated with percent urbanization. Comparisons across Panamanian rivers covered in a national survey to our focal rivers shows that saltwater intrusions and low DO of coastal swamp rivers may result in their classification by a standardized water quality index as having slightly contaminated water quality, despite this being their natural state. Examination of deforestation over the last 20 years, show that changes were <10% in the focal catchments, were larger in the small mountainous catchments and suggest that in the past 20 years the physical and chemical characteristics of river water that contributes to Almirante Bay may have shifted slightly in response to these moderate land use changes. (See supplementary information for Spanish-language abstract).