•Sewage outburst led to a significant eutrophication of coastal water.•Coastal eutrophication enhanced microbial growth.•TEP are released during the later stages of microbial demise.•TEP are only partially removed by the pretreatment system.•TMP of the RO membrane increase by 10% seven days after sewage outburst. Sewage outbursts affect coastal environments as seawater is enriched with nutrients, organic matter and microbes, thus can potentially impair seawater reverse osmosis (SWRO) desalination. In this study, we evaluated how municipal sewage outbursts affect SWRO desalination in a pilot-scale system. To this end, feedwater characteristics (i.e., coastal water), the removal efficiency of organic foulants by a dual-media gravity filter, and cartridge micro-filtration were determined daily for 12 days. Permeate water flux was maintained constant during the study, while trans-membrane pressure (TMP) was automatically adjusted and continuously monitored. The results indicate that sewage outbursts caused an immediate (∼1 d) buildup of phyto/bacterioplankton biomass (up to 10-fold), and enhanced activity (maximal 30-fold) followed by an increase in transparent exopolymer particle (TEP) concentrations. After sewage addition, algal biomass was significantly removed by the pretreatment system (72–90%), while a considerable fraction of the bacterial biomass (42–65%) and TEP (53–65%) passed these procedures. The result was a negative impact on the desalination performance reflected by a significant increase (> 10%) in RO-TMP 7.5 d after the sewage addition. Our results indicate on a direct link between sewage outbursts, pretreatment efficiency, and SWRO desalination. Nevertheless, these findings can lead to new avenues for the development of science-based operational protocols to minimize the deleterious effects of abrupt sewage outbursts on SWRO desalination. Display omitted