Chlorination is widely used to prevent biological fouling in power station cooling water systems. It may impact non-target organisms both within the cooling system and after discharge (primary and secondary entrainment). However, there is a lack of data on the impacts of the low chlorine concentrations that occur in the discharged plume on marine phytoplankton community structure and function. We examine the impacts on natural phytoplankton communities of single and multiple exposures to chlorination at concentrations between 0.02 and 0.1 mg/L total residual oxidants (TRO). Low-level chlorination causes limited changes in diversity and has no impact on total biomass. However, changes in size structure and functional diversity quantified using flow cytometry do show a reduction in smaller cells, particularly eukaryote picophytoplankton. These impacts are not detectable using chlorophyll a concentration alone, so flow cytometry provides important additional information over more standard ecotoxicological methods. The effects are likely to be localised in the vicinity of the discharges (mixing zone) where the environmental quality standard (EQS) of 10 μg/L for chlorine is exceeded, but impacts on coastal food webs and biogeochemical cycles should be further evaluated.