There are only few modelling, or other studies done between loadings of P and N in the Baltic Sea and respective concentrations reported from the same period in the sea. Using transfer function (TF) models, we have earlier presented a chain of events between changes in the North Atlantic weather patterns and subsequent changes in the Baltic Sea runoff and salinity, mesozooplankton and, finally, herring growth. The same reasoning is in this paper hypothetically extended to general Baltic system regulation and the actual nutrient loading and concentrations in the sea. This study is divided into three main questions: 1) Will increasing the number of predictors (North Atlantic and arctic weather indices) in the TF exercise improve our understanding of the Baltic Sea system regulation? 2) Is it possible to model Baltic nutrient loading on the basis of climatic factors, and the runoff, and nutrient concentrations in the incoming water masses? and, 3) Is it possible to model nutrient concentrations in the sea using loading as the predictor ? We also studied horizontal (regional and basin wide) and vertical ( i.e. thermocline and halocline) scale effects in nutrient concentrations? Climate indices - had specific influence in the Baltic freshwater runoff regulation. The most obvious difference between models could be detected in observed time lags. Larger geographical area, in general, meant longer regulation effect, i.e. delayed response from weather effect to a response of freshwater runoff into the sea. On the other hand, in north-south direction, the northern areas showed lagged response indicating stronger winter effect in north and east. NAO was evidently the best index to explain general runoff regulation. AO showed inverse and much longer regulation response. Iceland SLP indicated weaker but very similar kind of regulation as NAO, but inversely. Also Hoburg wind speeds resembled very much the NAO regulation. Nutrient loading - Nutrient loading models indicated very strong coupling between nutrient loading and freshwater runoff . All models showed that loading had instant response to runoffs in every geographical area studied . Nutrient concentrations - The effect of tot-P loading can been seen in seawater surface layer total P concentrations, with a lag of about one year in the central Baltic Sea, and a bit longer in the Gulf of Bothnia. None of our models for nitrogen manifested any connection between the nitrogen loading and concentrations in seawater, regardless of the chemical form (organic/inorganic) of the substance.