1. Freshwater phytoplankton communities are currently experiencing multiple global change stressors, including increasing frequency and intensity of storms. An important mechanism by which storms affect lake and reservoir phytoplankton is by altering the water column’s thermal structure (e.g., changes to thermocline depth). However, little is known about the effects of intermittent thermocline deepening on phytoplankton community vertical distribution and composition or the consistency of phytoplankton responses to varying frequency of these disturbances over multiple years. 2. We conducted whole-ecosystem thermocline deepening manipulations in a small reservoir. We used an epilimnetic mixing system to experimentally deepen the thermocline in two summers, simulating potential responses to storms, and did not manipulate thermocline depth in two succeeding summers. We collected weekly depth profiles of water temperature, light, nutrients, and phytoplankton biomass as well as discrete samples to assess phytoplankton community composition. We then used time-series analysis and multivariate ordination to assess the effects of intermittent thermocline deepening due to both our experimental manipulations and naturally-occurring storms on phytoplankton community structure. 3. We observed inter-annual and intra-annual variability in phytoplankton community response to thermocline deepening. We found that peak phytoplankton biomass was significantly deeper in years with a higher frequency of thermocline deepening events (i.e., years with both manipulations and natural storms) due to weaker thermal stratification and deeper depth distributions of soluble reactive phosphorus. Furthermore, we found that the depth of peak phytoplankton biomass was linked to phytoplankton community composition, with certain taxa being associated with deep or shallow biomass peaks, often according to functional traits such as optimal growth temperature, mixotrophy, and low-light tolerance. 4. Our results demonstrate that abrupt thermocline deepening due to water column mixing affects both phytoplankton depth distribution and community structure via alteration of physical and chemical gradients. In addition, our work supports previous research that phytoplankton depth distribution and community composition interact at inter-annual and intra-annual timescales. 5. Variability in the inter-annual and intra-annual responses of phytoplankton to abrupt thermocline deepening indicates that antecedent conditions and the seasonal timing of surface water mixing may mediate these responses. Our findings emphasize that phytoplankton depth distributions are sensitive to global change stressors and effects on depth distributions should be taken into account when predicting phytoplankton responses to increased storms under global change.