It has been observed that the momentum distributions of partons in bound nuclei are distorted relative to those of free protons and neutrons. This phenomenon was first observed in deep inelastic scattering experiments with muon and neutrino beams on nuclear targets and is known as the EMC effect. Similar phenomena have been observed in other high energy interactions such as the Drell-Yan process, the hadroproduction of direct photons, and the resonance production of charmonium and bottomonium states. In this work we investigate the possibility that these effects are predominantly of partonic origin. Standard nuclear quantum mechanics predicts that there is a non-zero probability for bound nucleons to overlap forming complex color singlets. We examine whether the observed EMC-type effects can be attributed to the difference between the parton momentum distributions in such clusters and those in single nucleons. We present a systematic way of determining these distributions in the Bjorken scaling limit and of estimating the average number of multiquark clusters in nuclei. The model predicts depletion of the valence quark and enhancement of the ocean quark and gluon components as the cluster baryon number increases. These properties can naturally explain significant features of the high energy behavior of nuclear targets.