<p>Benthic environments play a significant role in the biological productivity of the shallow coastal zone, with sandy sediments often understudied. As climate change affects coastal ecosystems (sea-level rise, storm surge and heat wave frequency), leading to increased interactions with the shoreline, it is vital to better understand coastal production and element cycling and the influences on them. In this study, monthly sampling was conducted over one year at three coastal sandy sites, of which one had outcropping peat layers. Various environmental variables were measured and primary production and nitrogen fixation rates were assessed. For that, stable isotopic tracer incubations were performed under both dark and light conditions to estimate heterotrophic and autotrophic rates. Additionally, nitrogenase sequences (nifH) from Baltic Sea metagenomic datasets were retrieved to examine and compare the taxonomic composition of the diazotrophic community. Benthic and pelagic nitrogen fixation rates ranged from 0.61 to 148.99 and 0.15–287.62 µmol N m^− 2 d^− 1, respectively. Primary production was about two orders of magnitude higher, suggesting that the productivity has a low dependency on nitrogen supplied by nitrogen fixation. The peat layer stations measured higher nitrogen fixation in the sediment, and an overall strong correlation with particulate matter was detected. The data also indicate that seasonal changes have a greater impact on pelagic than on benthic nitrogen fixation rates. This was also observed for the diazotrophic community composition, suggesting a well-adapted benthic community that maintains constant fixation rates from spring to autumn despite seasonal environmental changes.</p>