Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofauna state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a lregional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1,546 seafloor samples which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a sulfur oxidizer network (42.4% of samples, n=656), or an ammonium oxidizer network of microbes (44.0% of samples, n=681). Very few samples contained neither network (9.8% of samples, n=151), or both (3.8% of samples, n=58). Samples with a sulfur oxidizer network had a tenfold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a tenfold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01), and was present in all Icelandic samples (n=274). The ammonium oxidizer network was absent from Icelandic samples, and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 357 high-quality metagenome-assembled genomes (MAGs), we found that the main metabolic process for the ammonium oxidizer network was cobalamin-dependent, while the sulfur oxidizer network was associated with both ammonium retention and sulfur metabolism. In conclusion, our findings highlight the critical roles of sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor management.