The flocculation process of cohesive sediment impacts upon estuaries and tidal flats by affecting the sediment dynamics, modifying the biogeochemical exchanges, and playing an essential role in coastal ecosystems and geomorphologic evolution. To understand the roles of biological activity on flocculation processes in aquaculture areas, here we undertook in situ measurements over a bare tidal flat and a nearby clam aquaculture mudflat on the Jiangsu coast, China. Near-bed in situ floc size, the grain size distribution of suspended particles in seawater, suspended sediment concentration (SSC), and currents were obtained for nine consecutive semidiurnal tidal cycles simultaneously at the two sites. Correlation analysis indicated that the flocculation and its break-up process in this study appeared to be controlled by the variations in SSC and bottom shear stress due to combined wave and current. The floc sizes showed less difference between the two sites under calm conditions. However, the near-bed in situ floc size in the aquaculture mudflat was 23% larger than that in the bare tidal flat in the severe erosion events, suggesting modulation of the flocculation process due to the extracellular polymeric substances (EPS) eroded from the seabed sediments at the aquaculture site, as the hydrodynamics were very similar between the two sites. A higher EPS content was observed in the sediment layer below the surface seabed at the aquaculture site. We conclude that abundant filter feeders alter floc properties and enhance flocculation by excretion of exopolymer particles.