The composition of bacterial communities typically varies greatly in freshwater ecosystems, and the presence of toxic cyanobacterial blooms poses significant concerns for ecosystem and human health. In this study, we aimed to monitor the vertical bacterial community profile in a natural lake used for drinking water. We collected samples in March 2023 from the water column (surface, 1 m, 5 m, 10 m, 15 m, 20 m) where water is abstracted for the drinking water treatment plant. The bacterial community profile was examined by 16S rRNA amplicon sequencing using MinION Mk1C (ONT). The water temperature was 9.8°C ± 0.37, the dissolved oxygen level was 11 mg/L ± 1.44, and pH was 7.2 ± 0.27 as expected for the spring turnover period. The bacterial community was dominated by Cyanobacteria and its abundance decreased gradually throughout the water column in which the maximum abundance was 88% at the surface, while the minimum was 73% at 20 m. The result was in line with the historical data of this lake, showing that Cyanobacteria were an important component of the microbial community. The majority of the Cyanobacteria reads were assigned to Planktothrix rubescens. Toxic Planktothrix rubescens blooms have been observed in Lake Sapanca since the 1990s, highlighting the critical need for ongoing monitoring studies. Planktothrix agardhii and Synechococcus sp. were also detected at all depths. Moreover, the abundance of Pseudomonadota increased throughout the water column, reaching a maximum of 18% at 20 m. The results indicated that Cyanobacteria, which can produce toxins, taste, and odor, were abundant throughout the water column during the spring turnover together with Pseudomonadota and Actinomycetota species, which can degrade complex organic compounds. Since the study area is a drinking water resource, monitoring studies integrated with a metagenomics approach are needed to effectively mitigate Cyanobacteria blooms and microbial community dynamics.