We performed a study of the species diversity of Legionella in the northern Baltic Sea (Gulf of Bothnia) during early summer to map their occurrence and to identify possible environmental drivers. This study demonstrates the significance of DNA sequencing to map public health relevant bacteria like Legionella species in the environment. The dataset of the whole project consist of Illumina 16S rRNA V4 sequencing reads, full length 16S rRNA Nanopore sequencing reads and forward sequencing reads of Illumina 18S rRNA V6-V8 for eukaryotes.