Geochemical tracers were used to examine the mixing of water and particles in Lower New York and Raritan Bays in August 1999 during low-flow conditions. Four brackish water masses (20 ≤ S ≤ 28) originating in the Raritan and Shrewsbury Rivers, Arthur Kill, and Upper New York Bay were characterized by their dissolved metals concentrations. The mixing lines of dissolved Cu, Ni, and Pb in Lower New York Bay were similar to those in Upper New York Bay, the source of most of the freshwater to the system. Dissolved Cd and Mn seemed to have been removed by particles in several regions of the study. Dissolved Cu, Ni and Pb in the Raritan River fell below the mixing lines of the Lower New York Bay. In contrast, the concentrations of dissolved Co and Mn in the Raritan River were distinctly higher than those in the Lower New York Bay, while dissolved Cu and Ni were elevated in the Arthur Kill. A plot of dissolved Co versus dissolved Ni clearly differentiated among three water masses: (1) Upper and Lower New York Bays and Sandy Hood Bay, (2) the Raritan River, and (3) Arthur Kill–Raritan Bay–Shrewsbury River.

The concentrations of 22 elements also were measured in the suspended matter of Raritan and Lower New York Bays and brackish water sources. The elemental composition of the suspended matter in surface and bottom waters was correlated with Fe concentrations, which ranged between 50 and 900 μmol g^− 1. Statistical differences among the geographical regions were detected in the relationships of Ti, Ni, Co, As, and U with Fe, with particulate As being an especially strong geochemical indicator of Raritan River particles. The geochemical signatures of Lower New York Bay particles were similar to those of Upper New York Bay. The geochemical signatures of Raritan River particles were distinctly different than those of the Upper New York Bay, but the influence of Raritan River particles appeared to be limited to only inner Raritan Bay. This study illustrates the utility of trace elements for characterization of physical processes in complex estuaries.