The Binghamton metro area is the largest urban center within the predominantly forested headwaters of the NY region of the Chesapeake Bay watershed. It is likely that sources and fluxes of metals at different locations within the watershed reflect contributions from natural and anthropogenic processes. Monthly base flow sampling within the Chenango and Susquehanna Rivers was conducted during 2005 and 2006 for this assessment. Sampling occurred at sites on the Susquehanna River and Chenango River prior to entering the urban area, within the City of Binghamton at the confluence of the two rivers; and approximately 10 km downstream in Vestal, NY. Dissolved and particulate bound fractions were analyzed for major cations (DCP-AES) and anions (IC), and trace metals (HR-ICPMS). Distinct differences in the proportions of Sr, Ba, Mg and Na at the rural sampling sites within the Chenango and Susquehanna Rivers reflect differences in the contributions from carbonate and shale bedrock to ground water within the two watersheds. Superimposed over the ground water signature were differences in partitioning of Al, Mn, Fe and REE between particle and dissolved phases on a seasonal, spatial, and flow condition basis. This variation reflected differences in surficial erosional processes and rates within the watersheds. Enhanced levels of dissolved Rb, V, Ni and Mo during lowest flow conditions at the downstream location best document the trace metal signature from urban impacts superimposed over the natural geochemical variability in the river system.