Spectroscopically relevant properties in photosynthetic reaction centers change during charge separation. In this paper, we focus on incorporation of the complete set of environmental fluctuations in the modeling of the nonlinear spectra of molecular aggregates. The model is applied in simulations of two-dimensional electronic spectra of a photosynthetic reaction center at low temperature (5 K), where spectral lines are narrow, such that more features can be resolved. We show that vertical cross sections of the simulated two-dimensional spectra (with all populations in the lowest excited state) reveal transient hole-burned spectra excited resonantly within the B band in agreement with experiment, thus providing new insight into environmental fluctuation parameters of Rhodobacter sphaeroides at low temperatures. Correlated fluctuations of molecular parameters are found to be necessary to describe charge separated configurations of molecular excited states.