Cyanobacteria, as a substantial part of phytoplankton, play a key role in primary production in oceans and fresh waters. During their life, cyanobacteria cells needs to acclimate to a multitude of challenges, including shifts in a quality of underwater spectra. Recent progress in large scale environmental sampling and computational modelling provided insight into the effect of light spectrum on geographical distribution of cyanobacteria. However, detailed understanding to fitness advantage and limitations in the context of light quality has been missing. Here, we study photo-physiological acclimation in cyanobacterium Synechocystis sp. PCC 6803 through the whole range of photosynthetically active radiation (PAR). Using LEDs with qualitatively different narrow spectra, we describe wavelength dependency of light capture, electron transport rates and energy transduction to biomass, including fine-tuning processes such as state transitions and phycobilisomes attachment to photosystems. We show that growth was the most limited under blue light, due to extremely inefficient light harvesting. Even a low intensity of blue light induced PQ pool reduction and lead to the accumulation of reactive oxygen species. The PSI to PSII ratio was low under blue light, however, it was not the main limiting factor, since it was even more reduced under violet and near-far-red lights, where Synechocystis grew faster compared to blue light. Our results provide insight into the spectral dependency of growth in natural environments, and can provide a lead for light optimization in controlled cultivations.