To understand the spatiotemporal variability in the floc size distribution, the factors controlling floc size, and the timing of flocculation with sediment flux in the periodically stratified Geum Estuary, Korea, simultaneous measurements of current, salinity, suspended sediment concentration (SSC), and floc size distributions were analyzed and floc size was compared with stratification, turbulence, SSC, and sediment flux, Salinity measurements indicated that the water column was stratified during ebb and well-mixed during flood, consistent with the process of strain-induced periodic stratification. Coincident with periodic stratification was an ebb flood asymmetry in floc size where coarser, multimodal and variable distributions occurred during the stratified ebb whereas finer, unimodal and relatively constant distributions occurred during the well-mixed flood. Vertically, flocs coarsened downward during the stratified ebb and were vertically homogenous during the well mixed flood. The ebb-flood asymmetry in floc size was due to the ebb-flood asymmetry in stratification and turbulence. Furthermore, while floc size decreased with turbulence, the SSC increased with turbulence. As a consequence, large flocs occurred with relatively small ebb-directed fluxes whereas small flocs occurred with relatively large flood-directed fluxes. Overall, these observations indicate that the variability of the floc size distribution in periodically stratified estuaries is different than in well-mixed estuaries and that ebb-directed fluxes may be more flocculated than flood-directed fluxes in these systems.