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The concurrent goals of cement hydration are to percolate (bridge) the original cement particles into a load-bearing network and to depercolate (dam) the original water-filled capillary porosity. The initial volume, particle size distribution, and flocculation/dispersion state of the cement particles have a large influence on both hydration rates and microstructure development. Likewise, the capillary porosity as characterized by its pore size distribution, percolation state, and saturation state also influences both hydration kinetics and microstructure. In this paper, experimental techniques and computer modeling are applied to further understanding several of the critical connections between these physical parameters and performance properties. First, the setting or bridging process is explored via a combination of needle penetration and rheological measurements, in concert with three-dimensional microstructural modeling. Second, low temperature calorimetry is shown to be a valuable indicator of the percolation state or damming of the water-filled pores with various size entryways in the three-dimensional microstructure. Porosity percolation (or depercolation) is shown to be strongly influenced by both curing conditions and the alkali content of the cement pastes. Finally, it is proposed that future efforts in this field be directed towards a greater understanding of the (nano)structures of cement hydration products, particularly the calcium silicate hydrate gel, and their influence on performance properties.