Interactions between microfouling components influence the biofilm community and the cascading events, thus playing an important role in the biofouling process. Bacteria and diatoms are among the dominant forms reported in biofilms. Experiments were carried out with natural marine biofilms from a tropical monsoon-influenced environment to evaluate the interactions between bacteria and diatoms through application of antibiotics (streptomycin and chloramphenicol). Overall, chloramphenicol inhibited diatom communities, whereas streptomycin did not. These antibiotic-mediated changes in the fouling diatom community were consistent across the seasons. However, the rates at which the fouling communities changed depended on the initial species composition. It was also observed that elevated nutrient concentrations overrode the inhibitory effect of chloramphenicol. Maximum Vibrio enhancement was observed in the enriched conditions during the pre-monsoon and unenriched conditions during the monsoon (with naturally elevated background nutrient concentrations), highlighting the relevance of nutrient concentrations for Vibrio spp. This has interesting implications for antibiotic-mediated interactions between fouling diatom and bacterial communities under differing nutrient regimes. Although this study indicates the relevance of ‘cross-talk’ at the microfouling level, understanding the effects of additional microbial products (e.g. bacteriocins and peptidoglycan) on these community-level interactions will represent a step forward.