Coastal marine habitats become contaminated with the munitions constituent, Hexahydro-1,3,5-trinitro-1,3,5-trazine (RDX), via military training, weapon testing and leakage of unexploded ordnance. This study used ¹⁵N labeled RDX in simulated aquarium-scale coastal marine habitat containing seawater, sediment, and biota to track removal pathways from surface water including sorption onto particulates, degradation to nitroso-triazines and mineralization to dissolved inorganic nitrogen (DIN). The two aquaria received continuous RDX inputs to maintain a steady state concentration (0.4 mg L⁻¹) over 21 days. Time series RDX and nitroso-triazine concentrations in dissolved (surface and porewater) and sorbed phases (sediment and suspended particulates) were analyzed. Distributions of DIN species (ammonium, nitrate + nitrite and dissolved N₂) in sediments and overlying water were also measured along with geochemical variables in the aquaria. Partitioning of RDX and RDX-derived breakdown products onto surface sediment represented 13% of the total added ¹⁵N as RDX (¹⁵N-[RDX]) equivalents after 21 days. Measured nitroso-triazines in the aquaria accounted for 6–13% of total added ¹⁵N-[RDX]. ¹⁵N-labeled DIN was found both in the oxic surface water and hypoxic porewaters, showing that RDX mineralization accounted for 34% of the ¹⁵N-[RDX] added to the aquaria over 21 days. Labeled ammonium (¹⁵NH₄⁺, found in sediment and overlying water) and nitrate + nitrite (¹⁵NO_X, found in overlying water only) together represented 10% of the total added ¹⁵N-[RDX]. The production of ¹⁵N labeled N₂(¹⁵N₂), accounted for the largest individual sink during the transformation of the total added ¹⁵N-[RDX] (25%). Hypoxic sediment was the most favorable zone for production of N₂, most of which diffused through porous sediments into the water column and escaped to the atmosphere.