The influence of phytoplankton photoacclimation and adaptation to natural growth conditions on the chlorophyll a-specific in vivo absorption coefficient (a* _ph) was evaluated for samples collected in estuarine, coastal and oceanic waters. Despite an overall gradient in the physio-chemical environment from estuaries, over coastal, to oceanic waters, no clear relationships were found between a* _ph and the prevailing light, temperature, salinity and nutrient concentrations, indicating that short-term cellular acclimation was of minor importance for the observed variability in a* _ph. The clear decline in a* _ph from oceanic, over coastal, to estuarine waters was, however, strongly correlated with an increase in cell size and intracellular chlorophyll a (chl a) content of the phytoplankton, and a reduction of photosynthetic carotenoids relative to chl a. Variations in photoprotective carotenoids relative to chl a seemed to be of minor importance for the variability in a* _ph. In addition, significant differences in phytoplankton composition and abundance were observed, primarily driven by an increase in the abundance of diatoms, which furthermore correlated with increasing pigment packaging and decreasing a* _ph. The observed differences in a* _ph were, therefore, primarily driven by longer-term adaptations of the phytoplankton community. Our data suggests that an overall increase in nutrient loading from oceanic to estuarine waters increases phytoplankton abundance and favors larger sized species, particularly within the diatoms. These changes eventually decrease a* _ph through a rise in the package effect and a lower abundance of photosynthetic carotenoids relative to chl a.