Effective flocculation and dewatering of mineral processing streams containing colloidal clays has become increasingly urgent. Release of water from slurries in tailings streams and dam beds for recycle water consumption, is usually slow and incomplete. To achieve fast settling and minimization of retained water, individual particles need to be bound, in the initial stages of thickening, into large, high-density aggregates, which may sediment more rapidly with lower intra-aggregate water content. Quantitative cryo-SEM image analysis shows that the structure of aggregates formed before flocculant addition has a determinative effect on these outcomes. Without flocculant addition, 3 stages occur in the mechanism of primary dewatering of kaolinite at pH 8: initially, the dispersed structures already show edge-edge (EE) and edge-face (EF) inter-particle associations but these are open, loose and easily disrupted; in the hindered settling region, aggregates are in adherent, chain-like structures of EE and stairstep face-face (FF) associations; this network structure slowly partially rearranges from EE chains to more compact face-face (FF) contacts densifying the aggregates with increased settling rates. During settling, the sponge-like network structure with EE and FF string-like aggregates, limits dewatering because the steric effects in the resulting partially-gelled aggregate structures are dominant. With flocculant addition, the internal structure and networking of the pre-aggregates is largely preserved but they are rapidly and effectively bound together by the aggregate-bridging action of the flocculant. The effects of initial pH and Ca ion addition on these structures are also analyzed. Statistical analysis from cryo-SEM imaging shows that there is an inverse correlation of intra-aggregate porosity with Darcian inter-aggregate permeability whereas there is a strong positive correlation of Darcian permeability with settling and primary dewatering rate as a function of pH in suspension. Graphs of partial void contributions also suggest that it is not total porosity that dominates permeability in these systems but the abundance of larger intra-aggregate voids.