Absorption and emission spectra arising from the lowest energy transition in BODIPY have been simulated in the gas phase and water using a quantum mechanics/molecular mechanics (QM/MM) approach. Kohn-Sham density functional theory (DFT) is used to calculate both ground (So) and first excited (SI) states using the maximum overlap method to obtain the SI state. This approach gives ground and excited state structures in good agreement with structures found using multiconfigurational perturbation theory (CASPT2). Application of a post-self-consistent field spin-purification relationship also yields transition energies in agreement with CASPT2 and available experimental data. Spectral bands were simulated using many structures taken from ab initio molecular dynamics simulations of the ground and first excited states. In these simulations, DFT is used for BODIPY, and in the condensed phase simulations the water molecules are treated classically. The resulting spectra show a blue shift of 0.3 eV in both absorption and emission bands in water compared to the gas phase. A Stokes shift of about 0.1 eV is predicted, and the width of the emission band in solution is significantly broader than the absorption band. These results are consistent with experimental data for BODIPY and closely related dyes, and demonstrate how both absorption and emission spectra in solution can be simulated using a quantum mechanical treatment of the electronic structure of the solute.