This paper attempts to give a physical insight into the behavior of cavitation bubbles in a hydrodynamic cavitation reactor, with organic liquids employed as the bulk medium. The diffusion limited model of cavitation bubble dynamics has been coupled to hydrodynamics of flow through an orifice. Two kinds of bubbles, namely, air and argon, and two organic liquids, namely, n-hexane and toluene, have been chosen as the model system. The effect of four parameters on the dynamics of cavitation bubbles, namely, cavitation number, orifice to pipe diameter ratio, downstream recovery pressure, and initial bubble radius, has been investigated. Simulations show interesting results that dynamics of cavitation bubbles in organic media is relatively insensitive to operating parameters. These results have been attributed to physical properties of the organic media. Relatively, the intensity of the collapse of bubbles in toluene is higher than in hexane; however, the temperature peaks attained at the transient collapse of bubbles in both liquids are too low to allow formation of radical species in appreciable quantities. Hydrodynamic cavitation reactors with organic media are unsuitable for sonochemical reactions, although some physical processes or chemical reactions with external addition of source of radicals/ions may well be carried out.