The phenomenon of mucous macroaggregates, which periodically occur in late spring/early summer, was last seen in 2004. Colloidal organic matter (COM) acts as a precursor to such aggregates, which is why we focused on the seasonal dynamics of content, composition and molecular size of COM. We used 1H NMR and FTIR spectroscopy and HPSEC chromatography to observe changes in COM composition and size. The results showed that lipid fraction in COM increased towards summer, which may have impacted micro- and macrogel formation. The HPSEC demonstrated that COM aggregated from the winter to the summer months. HMW COM was the most abundant (95%). Conversely, the LMW COM, from winter to summer, decreased from 45% to 5%. In August, the ratio between the two fractions of COM was almost equal, which indicated either the formation of micro- and macrogels or that it was consumed via microbial degradation. Characterization of COM isolated from phytoplankton cultures from the Gulf of Trieste showed that phytoplankton mostly contributes, along with polysaccharides, to the COM pool. We used ICP-MS and CVAAS to observe the seasonal dynamics of metal content in the COM. Hg and Cu showed the highest metal affinity to COM, which was reflected in a positive correlation to COM. As with the COM content, Hg and Cu also rapidly decreased from July to August, which may have been due to either sequestration of the aggregates or increased microbial degradation in August. Data of the metal content from the salinity gradient of the Isonzo River showed that some metals occurred in the water column of the Gulf by desorption from particles transported by the river. Other metals, as well as COM, aggregated in the Isonzo River mouth because of increasing ionic strength, which was reflected in the lower metal content in the river mouth compared to the river.