## 2 Materials and Method
### Sentinel-2 Images Processing and Validation
For each image, the least represented class is rocks (b1) (not shown here), so we decided to combine the two classes b0 and b1 to obtain products characterized by two main classes: bare sediment (BS, b0 + b1) and rooted macrophytes (RM, b2). The maps related to each season were merged in average maps representative of the season, as suggested in [PERSON] et al. (2018) [62]. In detail, starting from the 34 maps, 17 seasonal maps were obtained (three for each year, except for 2015) to represent spring, summer, and autumn. The maps were composed by averaging each pixel value of the individual maps, considering both classes: BS and RM. Finally, in order to analyze the spatiotemporal variations of macrophytes communities, the main class RM was partitioned into two subclasses: dense macrophytes (D\({}_{\text{RM}}\)) and sparse macrophytes (S\({}_{\text{RM}}\)). Assuming that each pixel has a value between 0 and 1 (for both BS and RM), thresholds were estimated as follows: D\({}_{\text{RM}}\) (RM \(>\) 0.66), S\({}_{\text{RM}}\) (0.33 \(<\) RM \(<\) 0.66), and BS (RM \(<\) 0.33). The validation of the BOMBER outputs was performed analyzing optical closure error maps in two predefined ROIs: the first in an area (35 pixels, located in the west sub-basin) classified as colonized by macrophytes throughout the dataset, the second characterized by a constant absence of submerged vegetation (90 pixels, located in the \begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Seasons** & & \multicolumn{4}{c}{**Date**} \\ \hline \multirow{2}{*}{Spring} & NA & 23/03/2016 & 28/03/2017 & 23/03/2018 & 23/03/2019 & 24/03/2020 \\  & NA & 19/04/2016 & 17/05/2017 & 22/04/2018 & 17/04/2019 & 23/04/2020 \\ \hline \multirow{2}{*}{Summer} & 04/07/2015 & 28/06/2016 & 03/07/2017 & 18/06/2018 & 13/06/2019 & 02/06/2020 \\  & 03/08/2015 & 17/08/2016 & 02/08/2017 & 23/07/2018 & 23/07/2019 & 27/07/2020 \\ \hline \multirow{2}{*}{Autumn} & 12/09/2015 & 19/09/2016 & 21/09/2017 & 19/09/2018 & 14/09/2019 & 30/09/2020 \\  & 25/09/2015 & 16/10/2016 & 16/10/2017 & 04/10/2018 & 11/10/2019 & 08/10/2020 \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Sentinel-2 images used for each year and sorted by season. east sub-basin) (Figure S1). To identify these two ROIs, all maps depicting macrophytes meadows (RM > 0.33) and all maps relating to the bare sediment (RM < 0.33 or BS > 0.66) were intersected. Once identified, the mean value of the ROIs and standard deviation were calculated for the entire dataset. In order to study the pattern of bottom cover classes in relation to distance from the coast, six transects were created, three on each side of the coast (Figure 1). Along each transect, every 100 m, ROIs (3 \(\times\) 3 pixels) were created for a total of 38 ROIs. The ROIs were then applied to the seasonal maps to obtain the dominant bottom cover class. In detail: transect T1 (500 m) represents a port area characterized by large red beds; transect T2 (400 m) is in the proximity of a red bed area; transect T3 (500 m) crosses the route of the ferry that brings tourists to Sirminone (in Figure 2, a semicircle area lacking macrophytes can be observed in the northwest part of the mask of almost all seasonal maps); transect T4 (500 m) is located near a port and an urban area (car parking); finally, transects T5 (700 m) and T6 (1200 m) are located near port areas with a high presence of discharges from drains. Figure 2: Seasonal spatial distribution of the classes of bottom cover from 2015 to 2020: bare sediment (BS, brown), sparse macrophytes (SBM, light green), and dense macrophytes (DBM, dark green). Finally, we investigated the possible impact of the lockdown period (March to May 2020) on the density of macrophytes stands. In Italy, the first case of COVID-19 was detected on 21/02/2020, in Codogno (Lombardy). As a result, a number of restrictions were implemented to contain the spread of the virus.