The lagoons spanning Alaska’s Beaufort Sea coast provide a unique habitat for arctic wildlife. These lagoons and the food webs they support face extreme seasonality with nine months of ice cover followed by a spring thaw that pulses a large amount of freshwater and nutrients into the lagoons. Bacteria link these nutrients to the rest of the food web. Studying how microbes change in functional composition throughout the seasons provides insight into the biogeochemical processes occurring. Replicate water column samples were taken from three sites (two lagoons and one coastal) near Kaktovik, AK. Samples were taken in April, June, and August to represent winter, spring, and summer respectively, and size fractionated to separate free-living and particle-attached communities. Multivariate analysis of metagenomes indicated that seasonal variability in metabolic gene abundances was greater than differences between size fractions and sites, and that June differed substantially from the other months. We used DeSeq2, a negative binomial generalized linear model, to find differentially expressed genes between months along with indicator analysis to find indicator genes for each month. Broadly, we see seasonal changes in carbohydrate and energy metabolism as well as in environmental information processing. Winter samples taken in April appear to reflect a time of low energy inputs and autotrophic ba cterial metabolism, as there was increased detection of genes for carbon fixation and methane metabolism, nitrification, and Archaeal nucleotide processing genes. Nitrification and nucleotide processing genes belonged to Thaumarchaeota, suggesting this mixotrophic organism plays an important role in oxidizing ammonium in under-ice conditions. Despite previous work suggesting sediment denitrification rates on the western Arctic shelf do not change seasonally, we find June to have an increased abundance of indicator genes for denitrification, possibly linked to organic carbon availability. June also had indicator genes for pathways involved in processing phytoplankton derived organic matter, likely due to spring phytoplankton blooms. August samples had fewer indicator genes, but notably had increased abundances of anoxygenic photosynthesis genes. This study shows that estuarine microbial communities shift their metabolic functions between the extreme seasons of the arctic suggesting that these communities may be resilient to climate variability in a rapidly changing Arctic.