The inhomogeneous statistical associating fluid theory (iSAFT) is extended to associating polyatomic molecular systems, using the inhomogeneous form of the association functional. The approach provides an accurate method for modeling a wide range of complex associating polyatomic systems, capable of investigating the full range of association for any bonding scheme. Theoretical results demonstrate the ability of the theory to model problems near surfaces and in the bulk over a wide range of conditions. The examples chosen in this paper elucidate the importance of such a theory, highlighting how reversible bonding governs the structure of a fluid near a surface and in confined environments, the molecular connectivity (formation of supramolecules, star polymers, etc.), and the phase behavior of the system (including reentrant order disorder phase transitions).