SCIATRAN is a comprehensive software package which is designed to model radiative transfer processes in the terrestrial atmosphere and ocean in the spectral range from the ultraviolet to the thermal infrared (0.18–40 μm). It accounts for multiple scattering processes, polarization, thermal emission and ocean–atmosphere coupling. The main goal of this paper is to present a recently developed version of SCIATRAN which takes into account accurately inelastic radiative processes in both the atmosphere and the ocean. In the scalar version of the coupled ocean–atmosphere radiative transfer solver presented by Rozanov et al. [61] we have implemented the simulation of the rotational Raman scattering, vibrational Raman scattering, chlorophyll and colored dissolved organic matter fluorescence. In this paper we discuss and explain the numerical methods used in SCIATRAN to solve the scalar radiative transfer equation including trans-spectral processes, and demonstrate how some selected radiative transfer problems are solved using the SCIATRAN package. In addition we present selected comparisons of SCIATRAN simulations with those published benchmark results, independent radiative transfer models, and various measurements from satellite, ground-based, and ship-borne instruments. The extended SCIATRAN software package along with a detailed User's Guide is made available for scientists and students, who are undertaking their own research typically at universities, via the web page of the Institute of Environmental Physics (IUP), University of Bremen: http://www.iup.physik.uni-bremen.de.