Observations of Newark Bay, a sub-estuary network characterized by multiple junctions, reveal that fronts are generated by tidal flow through transitions in channel geometry. All fronts substantially contribute to along-channel estuarine heterogeneity, and most are associated with both changes in channel geometry and tidal velocity phase-shifts. A lift-off front forms at the mouth of the sub-estuary during ebb tide in response to the abrupt seaward channel expansion. While forming, the front is enhanced by a tidal velocity phase-shift; flood tide persists in the main estuary until 90 min after the start of ebb tide in the sub-estuary. A second lift-off front forms during ebb tide at a channel–side-channel junction and is enhanced by a lateral baroclinic circulation induced by baroclinic and barotropic tidal velocity phase-shifts between the main channel and side channel. The lateral circulation also bifurcates the along-channel ebb flow at the surface, generating a surface front above the lift-off front. At the head of Newark Bay, a second surface front forms during ebb tide at the confluence of two tributary estuaries. This confluence front is rotated across the mouth of the primary fresh water source by high velocities from the adjacent tributary estuary and is maintained through much of ebb tide by lateral straining and mixing. Although the overall stratification of Newark Bay would categorize it as a partially mixed estuary, the fronts divide the density structure of the sub-estuary into a series of nearly homogeneous segments—a characteristic that is more often associated with fjords.