Microbial electrochemical technologies have revealed the opportunity of electrochemical enrichment for specific bacterial groups that are able to catalyze reactions of interest. However, there are unsolved challenges towards their application under aggressive environmental conditions, such as in the sea. This study demonstrates the impact of surface electrochemical potential on community composition and its corrosivity. Electrochemical bacterial enrichment was successfully carried out in natural seawater without nutrient amendments. Experiments were carried out for ten days of exposure in a closed-flow system over 316L stainless steel electrodes under three different poised potentials (−150 mV, +100 mV, and +310 mV vs. Ag/AgCl). Weight loss and atomic force microscopy showed a significant difference in corrosion when +310 mV (vs. Ag/AgCl) was applied in comparison to that produced under the other tested potentials (and an unpoised control). Bacterial community analysis conducted using 16S rRNA gene profiles showed that poised potentials are more positive as +310 mV (vs. Ag/AgCl) resulted in strong enrichment for Rhodobacteraceae and Sulfitobacter. Hence, even though significant enrichment of the known electrochemically active bacteria from the Rhodobacteraceae family was accomplished, the resultant bacterial community could accelerate pitting corrosion in 316 L stainless steel, thereby compromising the durability of the electrodes and the microbial electrochemical technologies.