Heavy quarks and their bound states are ideal probes of the medium formed in heavy ion collisions. The hierarchy of scales of in-medium heavy quarkonium makes the combined system ideally suited for treatment using nonrelativistic effective field theories and the formalism of open quantum systems (OQS). In my talk, I will present an introduction to nonrelativistic QCD (NRQCD), potential NRQCD (pNRQCD) and the OQS formalism applied to in-medium heavy quarkonium. Using these tools, I will then present the derivation of the master equation governing the in-medium evolution of heavy quarkonium, discuss solutions of this master equation and present recent phenomenological results for the nuclear modification factor and the elliptic flow compared against experimental measurements.