Estuarine phytoplankton communities are acclimated to environmental parameters that change seasonally. With climate change, they are having to respond to extreme weather events that create dramatic alterations to ecosystem function(s) on the scale of days. Herein, we examined the short term (<1 month) shifts in phytoplankton communities associated with four pulse disturbances (Tax Day Flood in 2016, Hurricane Harvey in 2017, Tropical Storm Imelda in 2019, and Winter Storm Uri in 2021) that occurred in Galveston Bay (TX, USA). Water samples collected daily were processed using an Imaging FlowCytobot (IFCB), along with concurrent measurements of temperature, salinity, and chlorophyll-a. Stronger storm events with localized heavy precipitation and flooding had greater impacts on community composition, increasing diversity (Shannon–Weiner and Simpson Indices) while a cold wave event lowered it. Diatoms and dinoflagellates accounted for the largest fraction of the community, cyanobacteria and chlorophytes varied mostly with salinity, while euglenoids, cryptophytes, and raphidophytes, albeit at lower densities, fluctuated greatly. The unconstrained variance of the redundancy analysis models pointed to additional environmental processes than those measured being responsible for the changes observed. These findings provide insights into the impact of pulse disturbances of different magnitudes, durations, and timings on phytoplankton communities.