There is an increasing interest in how harmful algal blooms affect seawater desalination plants. These plants are critical for supplying municipal drinking water in many arid regions. Blooms can increase the probability of clogging filters, which in turn can disrupt proper plant operations, resulting in temporary shutdowns. Changes in bacterial diversity can be used as predictors of localized algae blooms. In this work, we used high-throughput DNA sequence analyses to study bacterial diversity focused on an event of Akashiwo sanguinea bloom in December 2019 on the coast of Antofagasta, Chile, where desalination plants are located. We collected weekly samples of attached-algae bacteria (1.0 μm filter) and free-living bacteria (0.2 μm filter) offshore in Antofagasta city between November 2019 and January 2020. DNA was extracted from the samples and the resulting 16s RNA sequence diversity determined. The resulting data was used to compute alpha diversity indices, Principal coordinate analysis (PCoA), dendrograms, and community composition. We found the relative abundance of attached Cyanobacteria strongly decreased during the bloom whereas Epsilonproteobacteria increased in abundance. Also, relevant functions decreased in blooming in the free-living bacteria.