We analyzed long‐term time series of temperature, salinity, and dissolved oxygen (DO) concentrations collected along the Palagruža Sill transect (middle Adriatic) between 1952 and 2010. The data have been mostly collected on seasonal basis, allowing for extraction of seasonal signal from the series. By applying Self‐Organizing Maps (SOM) method, a kind of unsupervised neural network method, the processes on a decadal time scale emerged as the most relevant for changes of oceanographic properties in the middle Adriatic area. Sensitivity studies revealed that oceanographic patterns obtained by SOM were not sensitive to shortening of time series, to removal of data from one station or to removal of DO from the analysis. Simultaneous SOM‐based mapping of sea surface heights in the northern Ionian Sea, with these heights serving as a proxy for the Adriatic‐Ionian Bimodal Oscillating System (BiOS), revealed asymmetry between anticyclonic and cyclonic BiOS patterns and correlated the decadal oscillations in the middle Adriatic with the reversals in the BiOS circulation regimes. These reversals are found to either rapidly change oceanographic properties in the middle Adriatic (e.g., during the Eastern Mediterranean Transient) or to change them with a time lag of 2–3 years. The mapped connections may be used for a short‐time (a few years) forecasting of the Adriatic oceanographic properties or for mapping future climate decadal oscillations as seen by ocean climate models.