Abstract. Long-term time series of physical and chemical parameters collected between 1960 and 2010 along the Palagruža Sill transect, middle Adriatic Sea, have been investigated in terms of average water properties and their variability. Nutrients, especially orthophosphates, reached rather higher levels of concentration below the euphotic zone between 1991 and 1998, the highest in the investigated period. Simultaneously, the N:P ratio, which is normally larger than 25:1, decreased to values less than 16:1 in the euphotic zone, indicating a switch from typical phosphorus-limited to nitrogen-limited preconditioning of the primary production. Higher-than-usual nutrient levels, coupled with lower-than-usual temperature, salinity and dissolved oxygen, have been attributed to the intermediate inflow of the nutrient richer Western Mediterranean waters to the Adriatic, entering the Adriatic during the anticyclonic phase of the Bimodal Adriatic-Ionian Oscillation (BiOS). The BiOS and the Northern Ionian anticyclone have been uniquely strengthened by the Eastern Mediterranean Transient occurring in the early 1990s. The observed changes have a potential to impact the primary production and presumably the whole trophic chain in the Adriatic and were likely responsible for the observed fluctuation in abundances of various species and fish stock, indicating a high relevance of the observed physical processes.