Fig. 1: Transect sample points at a) Schlei, b) Darß-Zingster Bodden Chain (DZBC), and c) Eastern Transect (Stettiner Haff - Peenestream – Greifswalder Bodden - Rügener Boddens). Red circles: time-series sampling. Yellow circles: seasonal sampling. lB: Little Belt. gB: Great Belt. S: øresund. Sampling points are listed in Supplementary Tables S1 and S2.

a) the Schlei estuarine (Figs 1 and 2a) is a flooded sub-glacial channel, extending ca. 42 km from the major Baltic Sea coast line towards the inlands. The inner Schlei comprises the two larger basins of the “Kleine Breite” and “Große Breite”, while the outer Schlei at some sections resembles a wider river. Adjacent, several “Noors”, i.e. water bodies similar to lakes, are connected to the main Schlei often by just narrow outlets. The Schlei has one medium sized inflow, the Füsinger Au at Kleine Breite, and several small creeks entering along the whole length of the water body. The salinity gradient is linearly increasing from almost 0-3 psu at the inner Schlei (Burgsee and Kleine Breite) towards values of ca. 15-20 psu near the outflow to the Baltic Sea (Gocke et al., 2003; Grupe, Heinrich, & Peters, 2009; LLUR. Schleswig-Holstein, 2001; Seiß, 2014). This gradient is seasonally influenced by relatively high freshwater discharge in winter and spring compared to summers. Additionally, episodic sea level changes by ± 0.5 – 1.5 m, caused by strong winds, lead to rapid movement of water masses within the Schlei, which superimposes the salinity gradient (Schulz, 1979). Saltwater intrusion events, from the North Sea into the Baltic Sea (Volker Mohrholz, 2018) (Fig 3) similarly have the potential to increase salinity values in the outer Schlei, as visible for March 2020 in contrast to July 2020 (Fig. 2a).

b) the Darß-Zingst Bodden chain (DZBC) is a system of several shallow water basins, which mostly do not exceed 2-3 m water depth (Figs. 1 and 2b). The rivers Recknitz and Barthe are major inflows and there are two outflows towards the Baltic Sea, which lie close to each other at the easternmost end of the Darß-Zingst peninsula. The salinity gradient is covering the range from almost freshwater conditions near the Recknitz and Barthe inflows to ca 10 psu near the outflows (Chubarenko, Chubarenko, & Baudler, 2005) . Those reflect the salinity values in the adjacent Baltic Sea, which are lower than in the more western realms (where the Schlei is situated), but likewise influenced by salt water intrusion events (Fig. 2b). The DZBC can be divided into an inner / western part (Saaler Bodden and Bodstedter Bodden), which is mainly influenced by riverine inflows and an outer / eastern part (Barther Bodden and Grabow) which is more susceptible to Baltic water inflow during conditions of east winds (Schumann, Baudler, Glass, Dümcke, & Karsten, 2006). The two parts are connected by the Zingster Stream (ZS), a narrow and deep water channel located in the central bodden chain.

c) the easternmost transect reaches from the Stettiner Haff, via the Greifswalder Bodden to the multiple lagoons which form the western and northern bodden chains around the isle Rügen (WRBC and NRBC) (Figs 1 and 2c). While the covered salinity gradient is similar than in the DZBC (i.e. 0 – ca. 10 psu), several inflows and connections to the Baltic Sea create a more dynamic system, in exchange with marine water widely overprinting the effects of freshwater inflow by rivers (Bachor, 2005; Correns & Jäger, 1979; H. Hübel & Dahlke, 1999; Helmut Hübel, Wolff, & Meyer-Reil, 1998)). The Stettiner Haff is strongly under influence of the Oder river, which contributes >95% of the riverine discharge along the northeastern German Baltic Sea coastline (Richter & Kowski, 1990). Salinity is gradually increasing between the Stettiner Haff, along the Peene-Stream towards the Greifswalder bodden (Fig. 2c) (Lampe, 1999). The latter is a larger basin of max 13.5 m depth which is separated to the open Baltic Sea by the “Greifswalder Boddenrandschwelle”, a glacial terminal moraine which builds a just 1 – ­2.5m deep shallow. The Greifswalder Bodden is connected to the WRBC by the Strela Sound, which terminates in the Vitter Bodden next to Hiddensee island. The same bodden can be seen as terminal basin of the inner or northern Rügen bodden chain (NRBC; reaching from Kleiner Jasmunder Bodden via Großer Jasmunder, Breeger, and Wieker Bodden), which is characterized by a salinity gradient from 0 to ca. 10 psu, comparable as in the DZBC (Birr; Ulrich Schiewer, 2008).