Hundreds of explosive-contaminated marine sites exist globally, many of which contain the common munitions constituent hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Quantitative information about RDX transformation in coastal ecosystems is essential for management of many of these sites. Isotopically labelled RDX containing ¹⁵N in all 3 nitro groups was used to track the fate of RDX in three coastal ecosystem types. Flow-through mesocosms representing subtidal vegetated (silt/eel grass), subtidal non-vegetated (sand) and intertidal marsh ecosystems were continuously loaded with isotopically labelled RDX for 16–17 days. Sediment, pore-water and overlying surface water were analyzed to determine the distribution of RDX, nitroso-triazine transformation products (NXs) and nitrogen containing complete mineralization products, including ammonium, nitrate+nitrite, nitrous oxide and nitrogen gas. The marsh, silt, and sand ecotypes transformed 94%, 90% and 76% of supplied RDX, respectively. Total dissolved NXs accounted for 2%–4% of the transformed ¹⁵N-RDX. The majority of RDX transformation in the water column was by mineralization to inorganic N (dissolved and evaded; 64%–78% of transformed ¹⁵N-RDX). RDX was mineralized primarily to N₂O (62–74% of transformed ¹⁵N-RDX) and secondarily to N₂ (1–2% of transformed ¹⁵N-RDX) which exchanged with the atmosphere. Transformation of RDX was favored in carbon-rich lower redox potential sediments of the silt and marsh mesocosms where anaerobic processes of iron and sulfate reduction were most prevalent. RDX was most persistent in the carbon-poor sand mesocosm. Partitioning of ¹⁵N derived from RDX onto sediment and suspended particulates was negligible in the overall mass balance of RDX transformation (2%–3% of transformed ¹⁵N-RDX). The fraction of ¹⁵N derived from RDX that was sorbed or assimilated in sediment was largest in the marsh mesocosm (most organic carbon), and smallest in the sand mesocosm (largest grain size and least organic carbon). Sediment redox conditions and available organic carbon stores affect the fate of RDX in different coastal marine habitats.