The main goal of the present study was to investigate the impact of the state of the environment on the microbiota of the wedge clam Donax trunculus (Linnaeus, 1758) from the region of Arkutino (Bulgarian Black Sea aquatory). The species Enterococcus hirae was isolated during the summer (from May to August). The species P. mendocina prefers the warmer months and the species P. alcaligenes the colder ones. The temperature followed a course of decrease during the period September 2020 to January 2021, followed by a slow increase from February 2021. Comparing May 2020 with May 2021, it became evident that in 2021 the temperature was 1.5 °C lower. We can say that the number of the species P. alcaligenes was twice as high in May 2021. It is likely that this species preferred lower optimum temperatures and constant other parameters. For the species Enterococcus hirae such dependence was not observed - the number remained constant in May, but with increasing temperature the number of microorganisms decreased during the summer months. The species seemed to preferably develop at pH 7.78. The species A. gyllenbergii preferably grows at temperatures between 20.3–25.7 °C and the optimal temperature was 25.7 °C. For C. farmeri the optimum conditions were temperature 26.2 °C and pH 7.3. The species E. vulneris was probably related not only to the increase in water temperature, but also to the anthropogenic factor, as it was found only in July.