Background
The basis for the eddy covariance (EC) technique is that turbulent mixing, caused by the interaction of current velocity with the benthic, atmospheric, sea-ice, or cline interfaces, is the dominant vertical transport process in boundary layers. Therefore, vertical fluxes across the ecosystem interfaces can be derived from high-resolution measurements of the vertical velocity and a solute concentration.

Field Sites
The field sites were located ~7 km offshore of Key Largo, Florida, USA at the southern tip of Florida in the Florida Keys. The sites were located on or adjacent to Little Grecian Rocks Reef with a site on the reef crest (25.119016°N, -80.300504°W) at 2.9 m mean depth, in a seagrass bed located ~225 m to the northwest of the reef site (25.120328°N, -80.302222°W) at 4.8 m mean depth, and in a sandy site located ~300 m to the southwest of the reef site (25.117320°N, -80.303069°W) at 6.3 m mean depth. The reef site is described in substantial detail (3-dimensional and species analyses) in Hopkinson et al. (2020), where the EC instrument can be seen near the center of the image analyses (in Figure 6 of Hopkinson et al. 2020) during its deployment in this study. This reef site is substantially degraded with its benthic surface and primary production dominated by octocorals, algae and rubble (Hopkinson et al. 2020). The seagrass site was dominated by dense Thalassia testudinum (turtlegrass) with a canopy height of 0.2 m underlain by carbonate sands. The sandy site was composed of carbonate sands with microalgal mats and migrating bedforms 0.1 m in height. Research was conducted from June 24 to June 29 in 2018 with the seagrass deployment beginning on the 24th and the sand and reef deployment beginning on the 25th of June, 2018.

Instrumentation
The EC systems used here, known as Eddy Covariance Hydrogen Ion and Oxygen Exchange System (ECHOES, Long et al. 2015) consisted of an Acoustic Doppler Velocimeter (ADV, Nortek) that was coupled to a FirestingO₂ Mini fiber-optic O₂ meter with a fast-response (~ 0.3 s) 430 µm diameter optode (Pyroscience) (Long et al. 2015, Long and Nicholson 2018, Long et al. 2019) and a fast-response (~0.6 s) Honeywell Durafet III pH sensor with a preamp Cap Adapter and a custom isolation amplifier (based on Texas Instruments ISO124P). The ECHOES systems logged the three-dimensional velocity, depth, O₂ optode, pH sensor, and triaxial Inertial Measurement Unit (IMU, MicroStrain model 3DM-GX3) at a frequency of 32 Hz continuously.

A separate frame at each site contained an Odyssey (Dataflow Systems, New Zealand) photosynthetically active radiation (PAR) sensor and a Seabird SeapHOx (measuring salinity, temperature, depth, O₂, and pH). The SeapHOx was factory calibrated and the Odyssey PAR sensors were calibrated to a HR-4 spectroradiometer system (HOBI Labs HydroRAD-4) using the methods of Long et al. (2012).

Refer to the Supplemental File "ECHOES_methods_FL2018.pdf" for more details on methdology.

Fl_par.csv