The effect of UVB radiation (UVBR, 290–320 nm) on the dynamics of the lower levels of the marine plankton community was modeled. The model was built using differential equations and shows a good fit to experimental data collected in mesocosms (defined as large enclosures of 1500 L filled with natural marine waters). Some unexpected results appear to be possible by indirect effects in prey (bacteria, phytoplankton and heterotrophic flagellates). In particular, apparent competition appears between small phytoplankton and bacteria. This effect is caused by a shared predator (ciliates). Another remarkable effect is an increase in bacteria and flagellates populations due to enhanced UVBR. This effect is similar to that observed under mesocosm experimental conditions and is related to the decrease of predation due to the direct damage to predators (ciliates) by UVBR. The effect of UVBR changing interaction coefficients may be dramatic on the community structure, producing big changes in equilibrium populations, as demonstrated by sensitivity analysis of the model. In order to generalize these results to field conditions it will be necessary to increase model complexity and include extra organic mater sources, mixing and sinking effects and predation by large zooplankton. This work shows that UVBR may produce community global responses that are consequence of both direct and indirect effects among populations.