High-resolution optical imaging systems are quickly becoming universal tools to characterize and quantify microbial diversity in marine ecosystems. Automated detection systems such as convolutional neural networks (CNN) are often developed to identify the immense number of images collected. The goal of our study was to develop a CNN to classify phytoplankton images collected with an Imaging FlowCytobot for the Palmer Antarctica Long-Term Ecological Research project. A medium complexity CNN was developed using a subset of manually-identified images, resulting in an overall accuracy, recall, and f1-score of 93.8%, 93.7%, and 93.7%, respectively. The f1-score dropped to 46.5% when tested on a new random subset of 10,269 images, likely due to highly imbalanced class distributions, high intraclass variance, and interclass morphological similarities of cells in naturally occurring phytoplankton assemblages. Our model was then used to predict taxonomic classifications of phytoplankton at Palmer Station, Antarctica over 2017-2018 and 2018-2019 summer field seasons. The CNN was generally able to capture important seasonal dynamics such as the shift from large centric diatoms to small pennate diatoms in both seasons, which is thought to be driven by increases in glacial meltwater from January to March. Moving forward, we hope to further increase the accuracy of our model to better characterize coastal phytoplankton communities threatened by rapidly changing environmental conditions.