Along with temperature, another factor that affects the physical characteristics of water is salinity. The salinity of Vanhankaupunginlahti fluctuates heavily due to run-off from the river Vantaanjoki and the more saline waters pushing in from the sea. Early in the year, the surface water is composed almost entirely of fresh river water, with salinity increasing towards the summer as run-off from the river decreases. As is typical in estuaries, the waters of Vanhankaupunginlahti occasionally form layers, so that the water near the bottom of the bay is much more saline than the surface water. This is caused by the fact that saline seawater flows into the bay along the bottom, while the fresh river water drains out of the bay along the surface.
The long-term development of Vanhankaupunginlahti’s summertime salinity follows the development of the salinity of other water areas off the coast of Helsinki. Water salinity was at its highest in the 1960s and 70s and has been decreasing since the 1980s. However, the fluctuation in summertime salinity is considerably higher than in Helsinki’s other sea areas. The low salinity and its fluctuation limit the occurrence of aquatic species in Vanhankaupunginlahti, and is an indicator of the impact that the variation in the ratios of river water and seawater has on the area.