For decades of human activity, particularly in the second half of the 20th century a large load of metals has been deposited in sediments of water bodies. It is important to identify processes determining their origin, pathways, distribution, and seasonal dynamics. This was studied in the Vistula Lagoon, second largest lagoon of the southern Baltic. A significant effect of wind on the magnitude and variability of concentrations of metals in the shallow lagoon was observed. It determined the supply of the elements from land (mainly Mn, Zn, U, Co) and distribution within salty Baltic waters (Co, V) from more polluted areas. Another process affecting circulation of metals in estuaries was flocculation. It contributed to vertical transport of Pb, Al, Fe, Mn, Cd, and Be to the sediment surface. Changes in their concentrations were observed, largely due to their remobilisation from land and sediments. It may consequently allow their inclusion into the food-web, particularly: Pb, U, Co, Be, Zn, Se, Cr, Sr, Ca, Al, Fe, Ni and Mg. The amount and type of accumulated metals in the cells were different for each phytoplankton group and cell size. The critical role was played by cyanobacteria algae Oscillatoriales. Not consumed degrading organic matter becomes a source of dissolved Pb, Ni and Mn in water.