During the last century, human activities have exerted an increasing pressure on coastal ecosystems, primarily inducing their eutrophication, with a more recent partial mitigation of this phenomenon where improvements of environmental management practices were adopted. However, a reanalysis of the pressures on coastal zones and surrounding drainage basins is needed because of the alterations induced nowadays by the climate changes. A comparative analysis of long-term oceanographic and environmental data series (1986–2018) was performed, in order to highlight the effects of anthropogenic and climatic disturbances on the phytoplankton community in the Gulf of Trieste (GoT). After the 1980s, the decline in phytoplankton abundance was matched to increasing periods of low runoff, an overall deficit of the precipitation and to a decrease in phosphate availability in the coastal waters (−0.003 µmol L−1 yr−1), even in the presence of large riverine inputs of nitrogen and silicates. This trend of oligotrophication was reversed in the 2010s by the beginning of a new and unexpected phase of climatic instability, which also caused changes of the composition and seasonal cycle of the phytoplankton community. Beyond the management of nutrient loads, it was shown that climatic drivers such as seawater warming, precipitation and wind regime affect both nutrient balance and phytoplankton community in this coastal zone.