For a long time, most studies about pyrite have focused on sediments while only a few have focused on pyrite in water. In this study, a method that combines the scanning electron microscopy (SEM) and the energy dispersive X-ray spectrometry (EDS) was used to compare pyrite particles suspended in water to those in associated bottom sediments, both obtained from the mixing zone of the Yangtze Estuary. It was found that the pyrite particles in the two media have similar morphologies and size distributions. The particle morphology mainly includes two types, single crystal and aggregate, and the particle size mainly ranges from 0.5 to 2 µm. The pyrite particles in water exhibit an increase in relative content towards the sea, and their transport and deposit processes are mainly affected by hydrodynamic conditions. It is concluded that the pyrite particles in the suspended matter mainly derived from the resuspension of sediments, which are products of the early diagenesis. Precursor minerals may appear during the formation of pyrite, but are generally restricted by the diagenetic environment and local microenvironment.