During the last decades, a decrease in the nutrients and an increase in marine temperature on the surface of the Varna Bay of the Black Sea have been registered. The main aim of this study was to establish the influence of some environmental factors (SST, TP, DIN) on the structure of the phytoplankton and to define what part of these dynamics results from the changes in temperature. Bivariate correlation and Nonlinear regression analyses were used to establish the connection between factors of the environment and the quality parameters of different size and taxonomic groups of phytoplankton. The rising SST proved to statistically significantly influence the decrease in the abundance of nano-phytoplankton (50.9%), the abundance and biomass of micro-phytoplankton (53%; 33.2%), the Bacillariophyceae (49.5%; 35.6%), and the biomass of the species of group “Other” (51.4%). The decreasing TP has a significant influence on the decrease in the abundance and biomass of the diatoms and the biomass of group “Other”. The decreasing DIN significantly affects the decrease in the abundance and biomass of Dinophyceae. The analyses showed that rising temperatures had a leading role in the changes in the taxonomic and size structure of phytoplankton during the period 1992–2019.