River estuaries are characterized by mixing processes between marine water masses and freshwater inflows depleted in heavier stable isotopes. Therefore, they often show a linear correlation between salinity and water isotopes (δ ¹⁸O and δ ²H values). In this study we evaluated spatial and seasonal isotope dynamics along three estuarine lagoon transects, located at the northern German Baltic Sea coast. The data show strong seasonality of isotope values, even at locations located furthest from the river mouths. They further reveal a positive and linear salinity-isotope correlation in spring, but hyperbolic and partially reverse correlations in summers. We conclude, that additional physical processes such as evaporation from the shallow lagoons, partially overprint the two-phase mixing correlation during summers. Understanding those water isotope and salinity dynamics are crucial in context of ecological studies. For example, when interpreting oxygen and hydrogen isotope data in aquatic organisms, that depend on ambient estuarine waters.