The flocculation mechanism dominates the fate of suspended matter in the estuarine environment. By modifying the texture of suspended matter, flocculation is one of the principle factors determining the transport and deposition of suspended matter in estuaries. Surveys of the seasonal variation of dispersed particle and non-dispersed particle characteristics, organic matter content as well as suspended matter deposition in two contrasting intertidal environments, one freshwater and one brackish water, in the Scheldt estuary were undertaken at fortnightly intervals for a year. The study of non-dispersed particle, i.e. floc, is mainly focused on floc size, shape, and microstructure, properties presumed to be significant in the suspended matter transport processes in the estuary. In this study, floc size as well as floc sphericity correlate positively with the change of organic matter content and reveal that floc grows in a three-dimensional way with increasing organic matter. It is observed that relatively condensed, small and elongated flocs appear in winter and spring periods, while loose, large and spherical flocs occur during the summer. The study also reveals that suspended matter transported as dense flocs with size range of ca. 105-250 μm have a greater effect on its short-term deposition than loose flocs with size range of ca. 250-500 μm. As the measured suspended matter deposition is much higher in winter-spring than in summer, it is deduced here that highly compact and relatively dense flocs contribute to deposition during winter and spring periods resulting in a stable layer, while loosely formed flocs likely lead to an easier erodible layer during the summer. This study concludes that floc structure-related density is a more significant parameter than floc size in the suspended matter deposition processes. © Springer 2005.