## 3 Materials and Methods
### Estuarine Mapping and Area Calculation  
Remote sensing imagery is a common resource to create thematic maps [18] and references therein. However, the use of satellite images often requires the definition of specific classifications for single images due to the differences in intrinsic characteristics (e.g., specific external conditions at the moment of the shot and angle and type of sensor, among others). Besides, publicly available remote sensing imagery have lower spatial and temporal resolution than aerial orthophotos (30 m/pixel compared with 0.25 m/pixel in some cases). For these reasons, this study developed on-screen digitization using visual image interpretation of different elements, i.e., colour, texture and plant association [41]. The three study areas (Figure 1) were mapped using historical aerial orthophotographs obtained from the Spanish National Plan of Aerial Orthophotography (PNOA), Andalusian Environmental Information Network (REDIAM) and Geological and Cartographic Institute of Catalonia (ICGC). The geodetic reference system used was the European Terrestrial Reference System 1989 (ETRS89-H30), according to the guidelines of the Geographic Superior Council, and following the INSPIRE European Directive (2007/2/CE). The orthophotographs of the first years of the study period (i.e., before the 2000s) were scanned and georeferenced in ArcGIS 10.2 through a second-order polynomial function, using at least 15 well-distributed control points on every image. The coordinates of these control points were taken from correctly georeferenced recent orthophotographs. The accuracy of the georeference process was determined by calculating the total Root Mean Square (RMS), less than 0.5 m in all cases. This type of analysis requires orthophotographs taken in low tide-conditions on clear days to easily identify and record the submerged features. Unfortunately, the number of images fulfilling these requirements is limited and it was necessary to soften the requirements to get enough data for this work. Therefore, some maps have a larger uncertainty than others and, as a consequence, the results must be interpreted with caution. Every feature was mapped through the study period with the Habitat Digitizer [42] extension to ArcGIS (ESRI(r)). Each feature was recorded with a unique ID, according to a hierarchical classification scheme (see below, Table 1), which was based on an extensive literature review. The use of unique IDs allows the habitat digitizer tool to easily define and assign attributes to polygons [43]. The maps were developed with a minimum scale of 1:2500. This delineates features with a limited surface but with enough relevance to have a role in the estuarine system. In addition, this tool allows setting a Minimum Mapping Unit (MMU, [44]), i.e., the minimum object identifiable in the image, and areas lower than 100 m\({}^{2}\) were not mapped. The hierarchical classification scheme was designed following three categories or levels of organization, from general to specific. (a) Category 1 represents the main subsystems within the estuary, common to every mid-latitude estuarine zone: Beaches, Dunes, Tidal Flats/Wetland, Channel and Rocky units. The first two subsystems encompass sandy environments, the third includes muddy environments (named with two different terms in order to differentiate between micro- and mesotidal environments), the fourth corresponds to the tidal drainage subsystem (which is a mix of sandy and muddy environments) and, lastly, the rocky units are only present in the San Vicente de la Barquera estuary. (b) Category 2 covers all of the features present in each subsystem of Category 1, defined mainly by Habitat Directive 92/43/CEE, EUNIS habitat classification and CORINE Land Cover classification. (c) Category 3 encompasses those features which need to be more specific than level 2. Thus, the hierarchical scheme is intended to be a standardized procedure to be applied in every estuarine zone of mid-latitude (Table 1).