Biotic interaction with complex communities of microbiota inhabiting every mucosal surface of teleost fish strongly influence the host metabolism, growth and health. The gill mucosal surface constitutes a special habitat for host-associated microbes due to its unique functions in waste excretion, gas exchange and local immune activity. The gill associated lymphoid tissue (GIALT) enables fish to discriminate between beneficial and pathogenic bacteria keeping microbiome homeostasis. Changes in the environment however, including water conditions, seasonal changes and physiological stress can lead to compositional disturbances that turn commensals into pathogens. This sensitivity to environmental parameters provides the opportunity to use the microbiome composition of the external mucus as a biomarker for the health of the fish. Here we compare the microbial gill mucus communities of the two teleost species Osmerus eperlanus and Gymnocephalus cernua from different life-history guilds and the bacterioplankton in the Elbe estuary. Over the course of one year, we collected 220 fish along the main channel of the estuary and generated matching 16S rRNA metabarcoding and host transcriptome libraries. The aim is to characterize the physiological response along spatio-temporal gradients, extract bacterial indicator species and determine driving factors for fish health.