We investigated whether climate change results in long-term changes in phytoplankton biomass and phenology in a turbid eutrophic coastal plain estuary. Changes in annual mean chlorophyll a (chla) concentrations were studied for the period 1978–2006 in the eutrophic and turbid macro-tidal Western Scheldt estuary. Three stations were investigated: WS1, at the mouth of the estuary; station WS6, halfway up the estuary; and station WS11, near the Dutch–Belgian border near the upstream end of the estuary. No significant long-term changes in yearly averaged chla concentrations were observed in WS1 and WS6, but in WS11 the phytoplankton biomass decreased considerably. This is most likely due to an increase in grazing pressure as a result of an improvement in the dissolved oxygen concentrations. Spectral analyses revealed a possible periodicity of 7 years in the mean chla which was related to periodicity in river discharge. We also observed strong phenological responses in the timing of the spring/summer bloom which were related to a well-documented increase in the temperature in the estuary. The fulcrum, the center of gravity or the day at which 50% of the cumulative chla was reached during the year, advanced by 1–2 days/year. A similar trend was observed for the month in which the maximum bloom was observed, with the exception of station WS1. All stations showed an earlier initiation of the bloom, whereas the day at which the phytoplankton bloom was terminated also moved forward in time excepted for WS11. As a result, the bloom length decreased at station WS1, remained the same at station WS6, and increased at WS11. This complicated pattern in bloom phenology demonstrates the complex nature of ecosystem functioning in estuaries.