## 2 Materials and Methods
### Field Data Collection and Laboratory and Numerical Analysis
#### 2.2.1 Characterization and Inventorying of the Transects  
In the first stage, a single permanent transect perpendicular to the main channel was established in the most extensive areas that presented adequate terrestrial accessibility (as they had to be surveyed by foot) and with the most overall coverage at each site in accordance with the previous field assessments in the context of this investigation, which was also based on a predefined permanent transect in Mira that we meant to monitor. The transects' topographic profile, z(m), was then registered using the Trimble R8s GNSS system (Table 1) and the soil elevation data was later used to determine hydrodynamic variables according to the procedure explained in Section 2.2.3.  
Quadrats were initially placed at the very beginning of the transects (at their highest elevation points as delimited by upward roads, at the furthest end from the water channel) and moved forward a meter at a time with its right side aligned with the soil elevation points that were measured. A total of 120, 50, and 70 m\({}^{2}\) were surveyed every month in Mira, Sao Jacinto, and Ilhavo, respectively. Each species was identified and had its cover-abundance determined according to the Braun-Blanquet (_B-B_) cover-abundance scale  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Strategy** & **Variables** & **Frequency** & **Analysis** & **Description** \\ \hline \multirow{4}{*}{Transect} & Elevation (z) & Once & & Measured directly with \\  & & & & a GPS-RTK on average every 0.6 m \\ \cline{2-5}  & Cover & & & All species were identified and \\  & abundance & Every month & & had their occupied area in an m\({}^{2}\) \\ \cline{2-5}  & Species & & & registered along the transect using \\  & diversity & & & a 1 \(\times\) 1 m quadrat \\ \hline \multirow{4}{*}{Transect} & Elevation (z) & & & Measured directly with \\  & & & & a GPS-RTK \\ \cline{2-5}  & Redox & & & Measured directly with a WTW \\  & potential (_Eth_) & & & pH 330/mV meter at 4 cm depth \\ \cline{2-5}  & & & & Measured with a WTW pH \\  & & & & 330/mV meter in the porewater \\  & & & & obtained from \\  & & & & sediment centrifugation \({}^{1}\) \\ \cline{2-5}  & & & & Measured with a WTW Cond 3110 \\ Main species & & & & SET 1 \\ monospecific stands (\(n\) = 5) & Salinity (PSU) & & & in the porewater obtained from \\  & & & & sediment centrifugation \({}^{1}\) \\ \hline Water & & & & Determined by drying 50 g of the \\ content (_WC_) & & & & collected sediment at 105 \({}^{\circ}\)C until \\  & & & & a constant weight was obtained \\ \hline Water depth (_WD_) & & & & \\ \hline Frequency of & & & Determined using a \\ flooding (_F_) & Every month & Numerical model & & hydrodynamic model developed \\  & & & & and calibrated for the \\  & & & & Ria de Aveiro lagoon [41] \({}^{2}\) \\ \hline \hline \end{tabular} \({}^{1}\) Centrifugation performed in a Thermo Scientific Heraeus Megafuge 16R Centrifuge, at 10,000 rpm for 5 min, at room temperature (about 21 \({}^{\circ}\)C). \({}^{2}\) Using numeric simulations regarding the annual period in which the campaigns took place (1 October 2021–31 September 2022).  
\end{table}
Table 1: Summary table of the different methodologies employed.  
(+ to 5) [42] and as a complement, the average coverage (_AC_) values attained by each species within the total sampled area of the transects were also calculated [43]:  
\[AC(\%)=\frac{Total\ cover}{Total\ sampled\ area}\]  
Once gathered, species distribution data were then used to calculate an elevation-dependent Shannon's entropy, \(S(z)\), for intervals within the full range of elevation of all three salt marsh transects [28]:  
\[S(z)=\ -\ \sum_{i=1}^{N}P_{i}(z)\ln P_{i}\ (z)\]  
where \(N\) is the total number of species in the salt marsh and \(P_{i}(z)\) is the probability that the \(i\)th species be in the established elevation interval.