Floc size, density, and settling velocity were investigated in the Connecticut River estuary over 3 years spanning varying fluvial discharge regimes to determine the role of cohesive suspended particle characteristics in the sediment-transport patterns of an energetic estuary. Concurrent measurements of flow, bed stress, salinity, and suspended sediment concentration were used to identify primary controls on floc size variability. Water discharge ranged from 202 to 910 m3/s between the three sampling campaigns, and the timing of major sediment-discharge events preceding measurement periods from 23 to 162 days. Two distinct particle populations were observed under high and low sediment-discharge regimes. With abundant fluvial sediment input, flocculation occurred resulting in large, loosely packed flocs dominating the suspended signal (median sizes of 194–209 μm; median excess densities of 13–17 kg/m3). Following an extended period of low sediment discharge, small, dense aggregates resuspended from the bed were observed throughout the water column (median size of 171 μm and excess density of 60 kg/m3). The timing and partial decoupling of water and sediment discharge led to inter-annual patterns of particle packaging controlled by fresh sediment supply. When the estuary is “charged” with sediment following high discharge events, the characteristic large, less dense flocs with lower settling velocities primarily bypass the estuary. The similar disaggregated grain size distribution of the suspended material of the two regimes suggests the same source sediment is reintroduced to the estuary with the intrusion of the salt wedge, which extends farther up-estuary during low-discharge regimes. The fines repackaged as dense aggregates ultimately supply the channel margins and off-channel coves currently experiencing sediment accumulation.