Temperature and ultraviolet radiation B (UVB) are expected to increase in the next few decades and will mostly affect mid and high latitudes. In order to study the combined effect of temperature and UVB increase, on the phytoplankton community in the Saint Lawrence Estuary, duplicates of four different treatments were applied to 2m3 mesocosms to simulate an overall 3°C and a 77.8% UVB increase, and combined. Samples were collected every 6h over 10days and the phytoplankton community was then analysed using a conventional flow cytometer and a Cytosense flow cytometer. Flow cytometry distinguished 9 clusters (Pico, Nano I, C3, C4, CHAINS, C6, C7 and C8) of cells sharing similar optical properties with average sizes varying from 1.3μm up to 101μm for chain forming cells. Compared to untreated enclosures, the high UVB treatment induced lower cell abundances (up to −40%) for clusters Pico, Nano I, C4, CHAINS and C7, followed by an unexpected cell abundance increase in all the clusters during the last 3days of the experiment (up to 46%). This increase was sustained by faster calculated periodicities of the cell optical characteristics and abundances, linked to a shorter cell cycle. In the samples from the high temperature treatment mesocosms, a positive delay was observed for the cell abundance increase in clusters CHAINS, C6 and C8, combined with higher average abundance values (up to 67% with respect to untreated mesocosms). During the last 3days of the experiment, abundances decreased compared to the values observed in the high UVB mesocosms, with a slower trend in the periodicities, suggesting that high temperature inhibits the cell cycle. The combined temperature and UVB treatment emphasized the effects observed under high temperature treatments, maintaining temperature positive effects (i.e. higher abundances) on clusters C3, CHAINS, C6 and C8 suggesting a compensation from the positive temperature effects over the negative (i.e. lower abundances) UVB effects. Increasing temperature induced a negative effect on the abundance of clusters C4 and C7. In this case, trends in C6 and C8 cell periodicities were faster than under normal conditions while Nano I, C4 and C7 cycles were slower. Cells<3μm were negatively affected by the combined exposure (up to −55% compared to untreated mesocosms) while most of the larger cells were positively affected (up to 75% compared to untreated mesocosms), suggesting a shift to an herbivorous food web (sensu). Results suggest that changes in cell cycles due to increases in temperature or UVB exposure may play an important role in controlling abundance.