Bacterial abundances in nearshore Mediterranean planktonic environments tend to change seasonally by 10-fold. Strong daily changes in bacterial abundance, at least as large as seasonal range, occurred in the presence of large dinoflagellate populations performing daily vertical migrations. The daily variability of heterotrophic bacteria was associated with the daily migrations of a bloom of Alexandrium taylori in La Fosca Bay, and Gymnodinium impudicum in Barcelona harbor. Bacterial abundance in surface waters can change daily as much as from 1 × 106 to 5 × 106 with apparent net change rates of 0.24 h−1. We suggest that the migrating dinoflagellates create microstructures exploited by the bacteria, and that the large algal populations (>106 cells l−1) make this microstructure visible with conventional sampling protocols. We also show evidence of the link between dinoflagellate abundance and relative bacterial activity in these waters, as measured by the percentage of bacteria with high nucleic acid content.