The Baltic Sea is a shallow, brackish, inland sea hosting several highly redox stratified basins with euxinic bottom waters. These sharp redox gradients closely juxtapose a diversity of substrates for microbial life, including reactions involving nitrogen species. During early spring 2024, an inflow of oxic, seawater from the North Sea disrupted the characteristically sharp redox gradients of the Baltic, offering a unique chance to examine how such perturbations impact resident nitrogen cycling processes through the lens of both natural abundance isotopes and ¹⁵N incubations. We present data from three stratified basins as well as from along the inflow front capturing the northward progression of redoxcline disruption. While ammonia and nitrite oxidation rates were closely coupled within established basin redoxclines, disruption by the inflow led to a marked decoupling, greatly enhancing ammonia relative to nitrite oxidation. Natural abundance nitrate isotopes captured the combined influence of both nitrate consumption and production occurring within both the basin redoxclines and disturbed inflow waters, including evidence for coupled nitrification and DNRA. While redoxcline N₂O production in the stratified basins was dominated by hybrid production (ostensibly by archaeal ammonia oxidizers), N₂O production in the disrupted redoxclines of the inflow exhibited a greater proportion of non-hybrid pathways suggestive of denitrification pathways. Metagenomic and metatranscriptomic data showcase functional expression of nitrogen metabolisms closely tracking oxygen in this disrupted redox system. As natural systems rarely exist in steady state, this work sheds light on the response of aquatic nitrogen cycling dynamics to disruptions in redox conditions.