What is the relationship between responses at the level of individuals, community dynamics and ecosystem processes (including productivity)? We aim at describing single organisms based on expressed phenotypic traits that directly respond to environmental changes, disturbance, pollution as well as eco-evolutionary processes like selection, competition or predation. We are deriving indices of trait-diversity based on individually acquired data to understand how individual responses scale to higher-level effects. We approach this challenge using scanning flow-cytometry and we have identified a set of focal phytoplankton traits that respond quickly and significantly to species interactions or environmental filters. Our results suggest that the description of functional diversity afforded by measured individual traits is extremely sensitive with regards to environmental change and tightly bound to productivity dynamics. We study how rapid changes in the environment affect the size and pigmentation of individual phytoplankton cells, because these traits tell us a lot about their physiology, ability to compete and avoid predators, as well as which species are present. By understanding the connection between these traits and the environment today, we hope to forecast how future environmental changes will affect the phytoplankton community, possibly predicting the whole lake processes.