The effects of changing hydrological and climatic conditions on the dynamics of phosphorus (P) were studied in the Northern Adriatic Sea (NA), a coastal system currently affected by these changes. P limitation is one of the key stresses in the NA and it is a globally important phenomenon in aquatic ecosystems. Therefore, the response to P stress by inducing alkaline phosphatase activity (APA) was studied in characteristic water types in the NA, formed by the changing freshwater input in different thermic conditions. APA was important in providing P for microbial growth in upper waters dominated by assimilation during the warmer part of the year in stratified conditions. Contrarily, APA was not important during mixing in the colder part of the year, as well as in waters dominated by regeneration. In waters influenced by freshwater, temperature had no effect on APA, while in high-salinity waters, temperature was an important factor for APA increase. The highest APA occurred during riverine nutrients supply, indicating that the alteration of anthropogenic nutrient loads might strongly change P status in this coastal system. Furthermore, predicted increases in winter sea temperature and summer Po River discharge could delay the water column mixing, prolonging periods of P limitation.