Particle concentration, charge, solution chemistry (i.e. ionic strength), and the nature of organic matter (OM) are the major factors controlling particle flocculation in aqueous environments. In the present study, the nature of clay fabric associated with clay–OM interaction at a range of ionic strengths was the focus. In the flocculation experiments, the aqueous suspension of montmorillonite and chitin was mixed with NaCl/MgSO4 electrolyte solution. Advanced sample-preparation techniques and visualization methods using transmission electron microscopy were used to observe directly the micro- and nano-scale clay–OM fabric of the resulting flocs. Such direct observation elucidated the role of OM in clay flocculation; few attempts have been made in the past due to the technical difficulties in preserving the original structure. A comparison of clay fabric at two different ionic strengths of 0 and 0.14 M revealed that the individual hexagonal clay particles settled slowly with little intra-aggregate void space (void ratio: 0.07) at 0 M while rapid flocculation and settling of clay particles at 0.14 M, with or without OM, resulted in a more open fabric with greater void space (void ratio: 0.33). The silver-staining technique demonstrated effectively the location of electron-transparent chitin in montmorillonite aggregates. Chitin appeared to link the face-to-face (FF) contacts of clay domains by bridging between negatively charged face surfaces. However, the resultant void ratio and the average hydrodynamic diameter (dH) values were lower than in the OM-free system after flocculation. The results indicated that the interplay between ionic strength and OM content affected the floc architecture and void ratio.