ABSTRACT: Coastal ecosystems typically comprise water patches of different salinities that host distinct communities of species. This salinity-driven heterogeneity can be vulnerable to changes in between-patch connectivity due to altered water levels. Despite the potentially grave implications for higher trophic levels, the impact of increased connectivity on phytoplankton assemblages is largely unknown. Here, we investigate the effect of increasing connectivity on assemblage resistance and recovery along a strong salinity gradient of 40-61 psu. We deployed mesocosms within a saltwork system and hydraulically connected enclosures of 3 salinity levels at 3 connectivity levels. We hypothesized that assemblage composition of high salinity would be more resistant to press invasions during connectivity; however, high connectivity would decrease compositional resistance and recovery irrespective of salinity. We found that high salinity assemblages were indeed more resistant and recovered better at low connectivity. High connectivity also impacted the function of high salinity assemblages by replacing large diatoms with small flagellates, preventing assemblage recovery. Counterintuitively, low salinity assemblage composition recovered better at higher connectivity, and this was attributed to rescue effects of rarer and stenohaline species within a more variable nutrient environment. Here, we show that normal (i.e. marine) salinity assemblages are vulnerable to anticipated changes in coastal hydrological regimes whereas higher salinity assemblages are impacted above a certain connectivity threshold.