Massive sea-dumping of chemical weapons (CW) is one of the aftermaths of World War II that implicates potential ecological consequences in modern times. Solely in the Baltic Sea, up to 60 000 tons of chemical warfare materials (CWM), containing up to 15 000 tons of sulfur mustard and arsenic-based chemical warfare agents (CWA) had been utilized mainly in the Bornholm Deep. Corroded munitions are now known to be leaking, resulting in sediments contamination with both intact parent compounds and known or newly-discovered transformation products. This results in the potential exposure of benthic and demersal biota to weaponized compounds that have only recently been recognized as toxic in the aquatic environment. This study aimed to investigate impact of Arsine Oil on sediment prokaryotic community abundance, structure, and metabolome. Sediments from two dumpsites and two reference areas were spiked with CW mixture of four arsenic-based agents in a quasi in-situ experiment. Sampling was performed at three time intervals: 0, 24 and 240 hrs, and targeted LC-MS, GC-MS and non-targeted UHPLC-HRMS, bacterial and archaeal 16S rDNA amplicon sequencing and qPCR were performed. Control samples from Borhnolm Deep were already contaminated, indicating recent leakage. Study results revealed environmental transformation of CWAs, substantial changes in microbial community structure, abundance, and exo-metabolome, uncovering unknown molecular pathways and outcomes. Supplementary data from ROV, AUV and sediment analyses allowed outcomes between CWA-contaminated and clean sites to be compared.