*2.6. Data Analysis of Hydrography and Flow*

Data visualization and CTD and ADCP data conversions were performed with Matlab R2018a. For subsequent data analysis, the raw CTD and ADCP data were converted. CTD variables were converted according to TEOS-10 standard with GSW Oceanographic Toolbox to absolute salinity (SA), conservative temperature (Θ), potential density (ρΘ) and potential density anomaly (σΘ), i.e., sigma-theta values [78,79]. The water column stratification was estimated from CTD casts with Brunt–Väisälä, or buoyancy, frequency

N2 = g2ρΘ−1ΔρΘΔz−<sup>1</sup> [79], where g is the gravitational acceleration and z is the depth. The flow measurements were corrected for the local magnetic declination based on International Geomagnetic Reference Field, IGRF-11 model data [80]. To estimate the mean flow direction, the horizontal velocity components (eastward, ue, and northward, un) were rotated using variance ellipses from the jlab data analysis toolbox [81]. Accordingly, the mean direction velocity components (um) are in the direction of the most energetic fluctuations, while components perpendicular are interpreted as cross-flow (uc). The vertical velocity component, uw, was not altered. The tidal frequencies, ω, and their amplitudes, a, were analyzed with the harmonic analysis toolbox T\_Tide [82]. The tidal signals were analyzed by using bottom pressure and horizontal velocity fields at 3 (SLM) and 5 (MLM) meters above the sea floor. Only signals with a signal-to-noise ratio >2 were considered to be significant.

The health statuses of the five included reefs were estimated using the known spatial extent of the reefs combined with data on density and vertical height of living coral colonies [15,22]. The flow state based on topography-flow interaction at the Nakken bank reef was determined following methods described in [22].
