Divalent nickel (Ni2+), Cu(II)EDTA, methyl orange, and dichromate were used to investigate diffusion from hydrated silica sol–gel monoliths. The objective was to examine diffusion of compounds on a size regime relevant to supporting biological components encapsulated within silica gel prepared in a biologically compatible process space with no post-gelation treatments. With an initial sample set, gels prepared from tetraethoxysilane were explored in a factorial design with Ni2+ as the tracer, varying water content during hydrolysis, acid catalyst present during hydrolysis, and the final concentration of silica. A second sample set explored diffusion of all four tracers in gels prepared with aqueous silica precursors and a variety of organically modified siloxanes. Excluding six outliers which displayed significant syneresis, the mean diffusion constant (Dgel) across the entire process space of sample set 1 was 2.42×10−10m2s−1; approximately 24% of the diffusion coefficient of Ni2+ in unconfined aqueous solution. In sample set 2, the tracer size and not gel hydrophobicity was the primary determinant of changes in diffusion rates. A strong linear inverse correlation was found between tracer size and the magnitude of Dgel. Based on correlation with the tracers used in this investigation, the characteristic 1-h diffusion distance for carbonate species relevant to supporting active phototrophic organisms was approximately 1.5mm. These results support the notion that silica sol–gel formulations may be optimized for a given biological entity of interest with manageable impact to the diffusion of small ions and molecules.