These lectures provide an overview of the theory of accretion disks with application to bright sources containing black holes. I focus on the fundamental physics of these flows, stressing modern developments and outstanding questions wherever possible. After a review of standard Shakura-Sunyaev based models and their problems and uncertainties, I describe the basic principles that determine the overall spectral energy distribution produced by the flow. I then describe the physics of angular momentum transport in black hole accretion disks, stressing the important role of magnetic fields. Finally, I discuss the physics of radiation magnetohydrodynamics and how it might affect the overall flow structure in the innermost regions near the black hole.
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