A display system includes a waveguide assembly having a plurality of waveguides, each waveguide associated with an in-coupling optical element configured to in-couple light into the associated waveguide. A projector outputs light from one or more spatially-separated pupils, and at least one of the pupils outputs light of two different ranges of wavelengths. The in-coupling optical elements for two or more waveguides are inline, e.g. vertically aligned, with each other so that the in-coupling optical elements are in the path of light of the two different ranges of wavelengths. The in-coupling optical element of a first waveguide selectively in-couples light of one range of wavelengths into the waveguide, while the in-coupling optical element of a second waveguide selectively in-couples light of another range of wavelengths. Absorptive color filters are provided forward of an in-coupling optical element to limit the propagation of undesired wavelengths of light to that in-coupling optical element.