The integron is a genetic element that incorporates mobile genes termed gene cassettes into a reserved genetic site via site-specific recombination. Known for their role in the spread of antibiotic resistance genes in Gram-negative bacteria, the integrons are found on numerous resistance plasmids housing multiple resistance gene cassettes and are thus largely responsible for conferring multi-drug resistance in clinically important bacteria. In environmental bacteria, integrons are found in chromosomal locations and can represent a major area of laterally acquired DNA. In Vibrio species, cassette arrays are large often containing hundreds of contiguous cassettes and making up 1-3% of the genome. Little is known about the role of this system in evolution and adaptation since the vast majority (~80%) of genes in vibrio arrays are highly novel and functions cannot be ascribed. Using biological assays andproteomic techniques, we determined how artificially engineered deletions in the cassette array of the model organism Vibrio rotiferianus, affected cell physiology. Deletion of gene cassettes (up to 46 out of 116 total) had a subtle effect on bacterial metabolism but significantly altered host surface polysaccharide most likely thorough addition of functional groups. Deletion (and most probably rearrangement and acquisition) of gene cassettes may provide the bacterium with a mechanism to alter its surface properties, thus impacting on phenotypes such as biofilm formation. Indeed, a deletion mutant had altered biofilm formation capabilities. This study provides exciting new data into the role of the integron in Vibrio species. We propose that reworking of surface polysaccharide is likely to provide an advantage in the environment and may assist the bacterium’s interactions with organisms such as bacteriophage, protozoan grazers or zooplankton.