The Pamlico and Neuse River estuaries, in North Carolina, display similar physical characteristics because of their proximity and physiographic setting. Yet, because of channel configuration and longitudinal alignment, differences in circulation and flushing exist. Spatially detailed hydrodynamic models were applied to each estuary to characterize these differences. The models were calibrated and tested using continuous records of water level and salinity collected at 15-minute intervals at sites throughout each study reach. Data and model simulations indicate that the alignment of each estuary in relation to Pamlico Sound and the predominant wind directions have significant effects on circulation and transport within each system. The range in simulated flow at the mouth of the Neuse River estuary was nearly 25 percent greater than that simulated at the mouth of the Pamlico River estuary. Simulated cumulative transport for an 11-day period in June 1991 was also greater and more dynamic in the Neuse River than in the Pamlico River. Simulated currents were generally higher in the Neuse River than in the Pamlico River and the tracking of individual particles showed greater overall movement in the Neuse River.