The different chlorophyll and non-chlorophyll pigments associated with the photosystems all have different absorption spectra, either because the spectra of the different chlorophyll pigments are modified by their local protein environment, or because the accessory pigments have intrinsic structural differences. The result is that, in vivo a composite absorption spectrum of all these pigments is broadened and flattened such that a wider range of visible and infrared radiation is absorbed by plants and algae. Most photosynthetic organisms do not absorb green light well, thus most remaining light under leaf canopies in forests or under water with abundant plankton is green, a spectral effect called the "green window". Organisms such as some cyanobacteria and red algae contain accessory phycobiliproteins that absorb green light reaching these habitats.
In aquatic ecosystems it is likely that the absorption spectrum of water, along with gilvin and tripton (dissolved and particulate organic matter respectively), determines phototrophic niche differentiation. The six shoulders in the light absorption of water between wavelengths 400 and 1100 nm correspond to troughs in the collective absorption of at least twenty diverse species of phototrophic bacteria. Another effect is due to the overall trend for water to absorb low frequencies while gilvin and tripton absorb higher ones. This is why open ocean appears blue and supports yellow species such as Prochlorococcus, which contains divinyl-chlrophyll a and b. Synechococcus, colored red with phycoerythrin, is adapted to coastal bodies while red-absorbing phycocyanin allows Cyanobacteria to thrive in darker inland waters.