Quantitating explosive materials at trace concentrations in real-time on-site within the marine environment may prove critical to protecting civilians, waterways, and military personnel during this era of increased threat of widespread terroristic activity. Presented herein are results from recent field trials that demonstrate detection and quantitation of small nitroaromatic molecules using novel high-throughput microfluidic immunosensors (HTMI) to perform displacement-based immunoassays onboard a HYDROID REMUS100 autonomous underwater vehicle. Missions were conducted 2-3 m above the sea floor, and no HTMI failures were observed due to clogging from biomass infiltration. Additionally, no device leaks were observed during the trials. HTMIs maintained immunoassay functionality during 2 h deployments, while continuously sampling seawater absent without any pretreatment at a flow rate of 2 mL/min. This 20-fold increase in the nominal flow rate of the assay resulted in an order of magnitude reduction in both lag and assay times. Contaminated seawater that contained 20-175 ppb trinitrotoluene was analyzed.