The Louisiana Shelf in the Gulf of Mexico experiences recurrent bottom water hypoxia under summertime eutrophic conditions. The onset, maintenance, and breakdown of hypoxia are associated with dynamic microbial biogeochemical cycles. However, the distribution of microbial taxa and metabolisms across Shelf oxygen gradients remains under-characterized. We combined biogeochemical analyses of nitrogen (N) distributions and metabolic rates with metagenomic and metatranscriptomic analysis of summertime Shelf waters. Samples from an east-west transect during July 2012 revealed an inverse relationship between nitrite and oxygen concentrations, with concentrations exceeding 1 lmol L 21 at 50% oxygen saturation and reaching 4.6 lmol L 21 at the most oxygen-depleted sites. Historical data confirms that nitrite accumulation occurs frequently in this region both above and below the hypoxic threshold. Experimental incubations demonstrated a strong decoupling between the two steps of nitrification, with ammonia oxidation proceeding up to 30 times faster than nitrite oxidation under low oxygen. 16S rRNA gene, metagenome, and metatranscriptome sequencing revealed a diverse microbial community, stratified over shallow (< 10 m) depth gradients, with an enrichment of ammonia-oxidizing Thaumarchaeota genes and transcripts in deeper more oxygendepleted layers, and a comparatively low representation of sequences related to nitrite oxidation. A range of factors, including temperature and substrate availability, which may be linked indirectly to bottom water oxygen content, potentially drives decoupling of ammonia and nitrite oxidation on the Louisiana Shelf. Nitrite accumulation in hypoxic zones remains understudied and may have important effects on microbial nitrogen flux, algal dynamics, and production.