Monitoring studies and thermodynamic modeling were used to reveal the changes of inorganic chemical species of some water pollutants (nutrients and trace metals such as Fe, Mn, Zn, Cu, Cd and Pb) inthe river-estuary-sea water system. The case studies were two rivers, Kamchiya and Ropotamo, representing part of the Bulgarian Black Sea water catchment area, and having different flow characteristics. There were no major differences in inorganic chemical species of the two river systems. NO3(-) and NO2(-) chemical species showed no changes along the river-estuary-sea water system. Concerning phosphates six different species were calculated and differences between the three parts of the systems were established. The HPO4(2-) and H2PO4(-) species were found to be dominant in river waters. The H2PO4(-) species quickly decreased at the expense of HPO4(2-) and Ca, Mg and Na phosphate complexes in estuary and seawater. Trace metals showed a great variety of chemical species. Fe(OH)2(+) species prevailed in river waters, and Fe(OH)3(0) species--in sea waters. Me2+ and MeCO3(0) (Me = Cu, Pb) and PbHCO3(+) were dominant in river waters, while Cu(CO3)2(2-) and PbCl(-) species appear also in sea waters. Cd2+ species prevailed in river and estuary waters, and CdCln(2-n) (n = 1-3) species, in seawater. Free Zn2+ species predominated in all systems but downstream their percentage decreased at the expense of Zn phosphates, carbonates,sulfates and chlorides complexes. Only free Mn2+ species were dominant along the systems.