Plankton succession was studied in a hyper-eutrophic stratified estuary, Mariager Fjord, Denmark. Above the pycnocline (15 m) pH increased from 8.5 to 9.2 after 5 d of sunny weather due to high primary production. The protistan grazers were dominated by heterotrophic dinoflagellates and mixotrophic and heterotrophic ciliates. Metazooplankton was dominated by meroplankton, rotifers, and the copepod, Acartia tonsa, all with a relatively low biomass. Cirriped nauplii occupied the upper strata while polychaete larvae the whole water column. Bivalve larvae occurred occasionally above the pycnocline even at very high pH. In exposure experiments the mixotrophic ciliate Mesodinium rubrum was the least pH tolerant species, followed by Strombidium spp., which did not cope well with seawater pH >8.5. Some heterotrophic dinoflagellates were more tolerant with net growth at pH >9. The predominant rotifer Synchaeta sp. tolerated up to pH 9.5 and the copepod survived pH 10 but stopped producing eggs at pH 9.5 with unaffected egg hatching success. The polychaeta and cirripedia larvae tolerated pH 9.5, but bivalvia larvae showed decreased survival already at pH 8.5. Based on in situ distribution patterns and pH exposure experiments we suggest that pH indeed contribute to structuring zooplankton distribution.