Changes in the photo‐chemistry of Microcystis aeruginosa in response to light and mixing

• Here, variable to maximal chlorophyll fluorescence ratio (Fv : Fm) was used to determine light history of Microcystis aeruginosa colonies in a shallow, stratified lake. • As insolation increased, the lake stratified and M. aeruginosa colonies displayed a depression in Fv : Fm that became less severe with depth. In the afternoon, wind speed increased, entraining colonies and disrupting the discrete depth variable Fv : Fm response. The point where the photochemical response became homogenized allowed determination of the water friction velocity necessary to entrain colonies of M. aeruginosa (u* = 0.003 m s−1). • Rates of Fv : Fm depression were dependent upon the photon flux density, whereas the rate of recovery of Fv : Fm was dependent upon the historical photon density. • A model is presented which models Fv : Fm response to five mixing scenarios: a stratified water body with no motion and no vertical migration; a cell circulating within the surface mixed layer of the Torrens Lake; a nocturnally mixed water column, which stratifies at dawn, allowing vertical migration of positively buoyant M. aeruginosa colonies; organized motion with a Langmuir circulation; and a simulation of turbulent water motion.