The definition of surface T-WB types is the first milestone in the implementation of the WFD (Section 1.2, Annex II) [
21] to enable the establishment of appropriate reference conditions and to make a valid assessment of the ecological status of T-WBs. However, at the European level, many difficulties have been encountered in defining a general typology for transitional waters [
43]. In particular, in the Mediterranean ecoregion, typologies based on different descriptors have been proposed e.g., [
37,
43,
44,
45,
46,
47], but a common consensus is still lacking. An approach based on the composition of macrophyte assemblages was used in this study to test the validity of the Apulian transitional water types, considering that they are representative of other Mediterranean ecosystems. Our results highlighted that a typology based on salinity ranges accounts for the variability of macrophyte assemblages, as required by WFD. Salinity proved to be the main environmental factor driving both the distribution and the composition of macrophyte communities, confirming previous observations in other areas [
7,
10,
48,
49,
50,
51,
52,
53,
54,
55,
56]. In fact, although several geomorphological and hydrological factors can also play a determinant role in modelling macrophyte assemblages [
57,
58], salinity regime well-explained the variability found in the T-WBs along the gradient of salinity. This agrees with Pèrez-Ruzafa et al. [
1], which had also identified the salinity regime as an influential factor, highly affecting sessile organisms such as macrophytes. Despite the differences in morphology, depth and extension, as well as spatial distances among T-WBs, those within the same salinity class showed comparable macrophyte communities in most of the cases. The mesohaline community was mainly represented by the Charophyta
Spirogyra sp. and
C. baltica, which showed high selectivity for the mesohaline T-WBs (TG and CE), being only found in both the basins although they represent quite different environments in terms of physico-chemical features. In particular, the genus
Spirogyra confirmed its preference for nearly freshwater habitats [
59], while
C. baltica showed the ability to tolerate brackish waters with salinity up to 15 PSU [
60].
On the other hand, geomorphologically and hydrologically similar coastal lagoons, but of different salinity classes, showed significant differences in their macrophyte composition and once again salinity played a crucial role in influencing macrophyte assemblages, as well as in the classification of lagoon types. The polyhaline community was represented by the dominance of
Z. noltei, a species considered euryhaline [
61], which formed monospecific beds or coexisted with
R. spiralis. This angiosperm also characterized macrophyte assemblages of meso- to polyhaline waters of the Rodia lagoon in Western Greece [
27]. The macrophyte community of the euhaline type was mainly represented by the euryhaline
C. nodosa [
51] and other typical marine species, such as the brown algae
G. barbata and
Dictyota dichotoma (Hudson) J.V. Lamouroux, the green
Valonia utricularis (Roth) C. Agardh and the red
Spyridia filamentosa (Wulfen) Harvey, well adapted to a salinity range which is almost the same of the open sea. Among the most abundant species,
G. barbata and
C. nodosa proved to be widely spread in the euhaline T-WBs (PC, MP1 and MP2), forming secondary substrates for several species and enhancing biodiversity. Even though harboring some common marine taxa, the euhaline coastal lagoons examined in this study displayed the lowest average similarity and some differences in macrophyte spectra composition that can be related to morphological aspects, such as the shape of the lagoons, the depth of the basins and the sea/lagoon exchange features. For instance, PC is an almost elliptical bay (2 km
2), only partially delimited by a narrow peninsula which leaves a permanent connection with the open sea through a channel system about 700 m wide; its average depth is about 1 m [
62]. MP is over ten times larger than PC, with a surface area of 20.72 km
2, but it is a semi-enclosed basin divided into First Inlet (MP1 T-WB) and Second Inlet (MP2 T-WB), with a maximum depth of 12 and 8 m, respectively. However, only the First Inlet is in communication with the Ionian Sea through two channels, thus causing a reduced water exchange [
63]. Effectively, PC was almost exclusively colonized by marine taxa, most of which shared with the adjacent open sea assemblages [
64], indicating constant species recruitment from these habitats. On the contrary, MP1 and, especially, MP2 were also inhabited by species of more confined environments, such as
Chaetomorpha aerea (Dillwyn) Kützing and
Ulva rigida C. Agardh. The macrophyte community characterizing the hyperhaline type was mainly represented by
R. spiralis. The genus
Ruppia has long suffered a chaotic taxonomy, but recently the three species
R. maritima Linnaeus,
R. cirrhosa (Petagna) Grande and
R. spiralis Linnaeus
ex Dumortier have been considered as fully independent taxa [
65]. These authors underlined that many Mediterranean records of
R. cirrhosa can actually be referred to
R. spiralis, a more common European species occurring in brackish habitats. Our specimens matched the specific characteristics of this species; therefore, they are here reported as
R. spiralis. This species can be considered as the most “marine”
Ruppia in Europe [
65], with broader salt tolerance. In addition to the main species characterizing the different macrophyte communities, some opportunistic taxa revealed to be well adapted to salinity variations and occurred in all the salinity ranges. They mainly belonged to the orders Ulvales and Cladophorales (Chlorophyta) and Ceramiales (Rhodophyta).
Species Richness index was closely associated with salinity. Macrophyte diversity was the highest in euhaline T-WBs, which had salinity levels similar to marine waters, started to decrease in polyhaline T-WBs and reached minimum values at the two ends of the salinity range. This declining trend in the number of taxa, depending on too low or too high salinity, was already reported in Mediterranean coastal lagoons [
19,
52,
67] and in the Baltic Sea [
56,
68] and it was confirmed in the present study. The lowest species richness recorded in mesohaline and hyperhaline T-WBs, where salinity was quite far from marine waters, reflected stress conditions, with fewer species tolerating these extremes. The strongest reduction was observed in Rhodophyta, for which the number of species consistently dropped along the salinity gradient (75 in euhaline T-WBs vs 5 and 2 in hyperhaline and mesohaline T-WBs, respectively), with a reduction between 93 and 97%. The percentage of decrease in species number was still quite high in the Ochrophyta-Phaeophyceae (75–88%) and the lowest was displayed by Chlorophyta (49–77%). This pattern was also evident at order level. For example, some typical marine taxa, belonging to Corallinales or Gelidiales orders, not only were found in euhaline T-WBs but were also able to tolerate the lower salinity of polyhaline T-WBs; they completely disappeared in mesohaline and hyperhaline T-WBs, that were almost exclusively inhabited by opportunistic Ceramiales. The salinity ranges in these environments prevented large colonization by red algae and favoured the settlement of Chlorophyta, mainly Cladophorales and Ulvales, the best adapted to low-salinity and hyper-saline conditions [
69,
70]. Among Ochrophyta-Phaeophyceae, likewise, well-structured Dictyotales and Fucales species were found in euhaline and polyhaline T-WBs, while very few opportunistic species of Ectocarpales were the only present in the other T-WBs.