Throughout the cold and the warm periods of 2020, chemical and toxicological characterization of the water-soluble fraction of size segregated particulate matter (PM) (<0.49, 0.49–0.95, 0.95–1.5, 1.5–3.0, 3.0–7.2 and >7.2 μm) was conducted in the urban agglomeration of Thessaloniki, northern Greece. Chemical analysis of the water-soluble PM fraction included water-soluble organic carbon (WSOC), humic-like substances (HULIS), and trace elements (V, Cr, Mn, Fe, Ni, Cu, Zn, As, Cd and Pb). The bulk (sum of all size fractions) concentrations of HULIS were 2.5 ± 0.5 and 1.2 ± 0.3 μg m−3, for the cold and warm sampling periods, respectively with highest values in the <0.49 μm particle size fraction. The total HULIS-C/WSOC ratio ranged from 17 to 26% for all sampling periods, confirming that HULIS are a significant part of WSOC. The most abundant water-soluble metals were Fe, Zn, Cu, and Mn. The oxidative PM activity was measured abiotically using the dithiothreitol (DTT) assay. In vitro cytotoxic responses were investigated using mitochondrial dehydrogenase (MTT). A significant positive correlation was found between OPmDTT, WSOC, HULIS and the MTT cytotoxicity of PM. Multiple Linear Regression (MLR) showed a good relationship between OPMDTT, HULIS and Cu.