The influence of substrate physical properties on water transport and plant growth must be known if irrigation water use efficiency is to be improved. Three fundamentally different substrates were examined: 1 peat moss: 1 vermiculite (v/v), 3 pine bark: 1 peat: 1 sand, and 1 mineral soil: 1 peat: 1 sand. Capacity analyses included total porosity, container capacity, air space, available water and unavailable water. Water transport was characterized by saturated and unsaturated flow analyses. A new method, Pore Fraction Analysis, was developed to characterize substrate pore structure into fractions based on function with the substrate. This method is based on soil moisture retention curves, pore size distributions, and average effective suction at container capacity (AEScc) This method is offered to expand the traditional terms of macropore and micropore into new definitions: macropores, mesopores, micropore, and ultramicropore; each based on a range of pore sizes and functions. Computer simulation models of air and water profiles were run on several container sizes with the three test substrates. Pore fraction analysis indicated that under traditional production practices macropores indicate the volume of a substrate that be filled with air at container capacity, the mesopore fraction effectively fills and drains with daily irrigation, the micropore fraction functions as a measure of water reserve, while the ultramicropores contain water unavailable to the plant.