River estuaries are characterized by mixing processes between isotopically depleted freshwater inflows and isotopically more enriched marine water masses. Therefore, they often show linear correlation between salinity and water isotopes (δ18O and δ2H values). Here we evaluated spatial and seasonal isotope dynamics along three estuarine lagoon transects 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 even reverse correlation in summers. We conclude that additional physical processes, such as evaporation from the shallow lagoons, overprint the two-phase mixing correlation during summers. Understanding of those water isotope 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.