Despite extensive research into silica gels, little exists that describes the porous properties of the fundamental molecular sieving framework due to limitations of current characterization techniques. This paper describes the novel use of positron annihilation lifetime spectroscopy (PALS) for rapid quantitative measurement of sub-nanometer pores in amorphous molecular sieving silicas. The well-established N2 adsorption technique was also used, but most materials appeared nonporous as adsorption cannot detect pores less than the size of the N2 molecule. PALS, on the other hand, detected hierarchical trimodal porosity in all silicas, peaking at around 3, 8, and 12 Å. Gas permeation probing through membranes made using the same silicas verified the ∼3 Å size cutoff and provided strong evidence that the intermediate and larger pores are not continuously connected for large molecule diffusion. For these “sponge-like” silicas, all molecules must pass through the fundamental silica framework that provides the selectivity. The quantity and size of intermediate and large pores was in turn found to contribute to the permeation performance. A hydrostabilized templated silica had more intermediate and larger pore interconnection evident by high N2 adsorption and slightly lower selectivity than the same non-templated material. A material tailored for improved H2/CO2 separation had a reduced size of the smaller pores, which gave it better selectivity. Studies of temperature evolution of silica gels from 200–600 °C using PALS conclusively showed that temperature increases the pore size of the fundamental silica framework. This observation fits well with widely reported progressive network assembling via formation of siloxane groups causing the silica to “inflate”, which now describes in better detail the porous features of the fundamental silica network.