Spatial and seasonal 16S rRNA Dataset from gill mucus swabs of two estuarine wild fish species (Osmerus eperlanus, Gymnocephalus cernua). Fish were caught with a stow-net vessel at 5 stations along the salinity gradient between Cuxhafen and Hamburg, Germany. Sampling took place at 4 Seasons. Gill mucus was swabbed for fish and baterioplankton was determined from water filters (0.2µm Polycarbonate membrane, without pre-treatments). Sequencing on a Miseq, V3-V4, For-CCTACGGGAGGCAGCAG Rev-GGACTACHVGGGTWTCTAAT