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Although seagrass ecosystems are valued for the services they provide, anthropogenic impacts have led to global declines in seagrass area. South Florida harbors one of the most extensive and iconic seagrass landscapes in the world, but historic seagrass losses appeared to threaten their integrity. The establishment of the Florida Keys National Marine Sanctuary (FKNMS) in 1995 created a benthic community and water quality monitoring network to aid management efforts. With this study, we report on the status and trajectories of benthic communities in South Florida using 25 years of monitoring data. Overall, most of our permanent monitoring sites maintained stable benthic communities over the period of observation. However, for areas that did experience decline, we identified mechanisms for loss of the climax seagrass Thalassia testudinum in the FKNMS with no or only partial recovery over decadal timescales. We observed a shift towards fast-growing Halodule wrightii meadows at anthropogenically nutrient-enriched nearshore sites along the Florida Keys. In addition, we describe almost complete loss of seagrass meadows at some exposed, back-reef sites offshore from the Florida Keys resulting from physical disturbance by major hurricanes. This study demonstrates the utility of long-term monitoring programs for the identification of benthic community trajectories and their putative drivers on the seascape scale, offering valuable lessons for the design of future seagrass monitoring programs. 

Subtropical seagrass meadows play a major role in the coastal carbon cycle, but the nature of air–water CO₂exchanges over these ecosystems is still poorly understood. The complex physical forcing of air–water exchange in coastal waters challenges our ability to quantify bulk exchanges of CO₂and water (evaporation), emphasizing the need for direct measurements. We describe the first direct measurements of evaporation and CO₂flux over a calcifying seagrass meadow near Bob Allen Keys, Florida. Over the 78‐d study, CO₂emissions were 36% greater during the day than at night, and the site was a net CO₂source to the atmosphere of 0.27 ± 0.17 μmol m⁻²s⁻¹(x̅ ± standard deviation). A quarter (23%) of the diurnal variability in CO₂flux was caused by the effect of changing water temperature on gas solubility. Furthermore, evaporation rates were ~ 10 times greater than precipitation, causing a 14% increase in salinity, a potential precursor of seagrass die‐offs. Evaporation rates were not correlated with solar radiation, but instead with air–water temperature gradient and wind shear. We also confirm the role of convective forcing on night‐time enhancement and day‐time suppression of gas transfer. At this site, temperature trends are regulated by solar heating, combined with shallow water depth and relatively consistent air temperature. Our findings indicate that evaporation and air–water CO₂exchange over shallow, tropical, and subtropical seagrass ecosystems may be fundamentally different than in submerged vegetated environments elsewhere, in part due to the complex physical forcing of coastal air–sea gas transfer.