Rivers are progressively being exposed to increased anthropogenic pollution stresses that are undermining their designated uses and affecting sensitive coastal areas. In this study, three adjacent eastern Mediterranean coastal rivers, Ibrahim, Kaleb and Beirut, were evaluated. Water quality samples were collected in dry and wet seasons from different sampling sites along the river from the source to the outlet which represent a gradient of increased urbanization. The spatiotemporal variability of the physio-chemical properties, heavy metals (Zn, Pb, Cu, Cr, and Cd) and organic matter (DOC) were statistically analyzed to better understand the contribution of point and nonpoint pollution sources. The three rivers (Beirut, Kaleb and Ibrahim) show a similar behavior in calcium and carbonate alkalinity due to the carbonate mineral weathering effect, so they are of calcium bicarbonate type due to their calcareous geological nature. The speciation of anions was affected by temporal variation. Moreover, it is obvious that the Beirut River has a different behavioral characteristic where the water is a sulfate type water with a preferable metal-OM complexation mainly with lead, zinc and copper, whereas Kaleb and Ibrahim are considered to be of a nitrate phosphate type with a preferable metal inorganic complexation, especially copper, that has a consistent behavior in both types of waters. This difference is attributed to the urbanization effect highly impacting the Beirut River.