We develop a theory for the dynamics of the density matrix describing a multimode polariton condensate. In such a condensate several single-particle orbitals become highly occupied, due to stimulated scattering from reservoirs of high-energy excitons. A generic few-parameter model for the system leads to a Lindblad equation which includes saturable pumping, decay, and condensate interactions. We show how this theory can be used to obtain the population distributions, and the time-dependent first- and second-order coherence functions, in such a multimode condensate. As a specific application, we consider a polaritonic Josephson junction, formed from a double-well potential. We obtain the population distributions, emission line shapes, and widths (first-order coherence functions), and predict the dephasing time of the Josephson oscillations.