The primary goal of the work described in this dissertation was the incorporation of functionality into metal phosphonates. This was done in one of several ways. The first involved using phosphonate ligands that had covalently attached organic functional groups. In some cases, these ligands undergo reactions during the solvothermal syntheses which can impart new chemical reactivity. Another method used to introduce functionality was to partially or completely substitute metal atoms within phosphonate clusters to create materials which may have interesting magnetic properties. By controlling the way these clusters pack in the solids, their magnetic properties may be able to be augmented. The final method used to impart functionality to metal phosphonates was the incorporation of N-donor and bulky aryl groups into the phosphonate ligands. These influences caused structural variations which exposed potentially active sites within the materials, including both Lewis acidic and basic sites, as well as Bronsted acid sites. The first strategy was employed in the design of tetravalent metal phosphonates which have covalently incorporated bipyridine moieties. The materials are porous so that the bipyridine sites can chelate Pd atoms from solution, which can then be reduced to stable nanoparticles trapped within the phosphonate matrix. This approach was also used in the synthesis of surface-functionalized divalent metal phosphonates which exhibit interesting amine uptake properties. Solvent and cation substitution effects were used to control the packing and connectivity of phosphonate-based clusters. The selective substitution of metal atoms within the clusters may lead to interesting magnetic materials. In other work, N-donor and bulky phosphonates were used to influence the structure of several SnII phosphonates, which resulted in the discovery of a new layered structure type. The effect of the Sn-N interaction on the structures is investigated, and found to have significant effects on the structural units formed and how they pack in the solid state. The work presented herein represents only a small fraction of the rich chemistry of metal phosphonates. Creative researchers will continue to push boundaries and find new and interesting applications for phosphonate-based materials.