Significant security threats posed by highly energetic nitroaromatic compounds in aquatic environments and the demilitarization and pending cleanup of areas previously used for munitions manufacture and storage represent a challenge for less expensive, faster, and more sensitive systems capable of analyzing groundwater and seawater samples for trace levels of explosive materials. Presented here is an inexpensive high throughput microfluidic immunosensor (HTMI) platform intended for the rapid, highly selective quantitation of nitroaromatic compounds in the field. Immunoaffinity and fluorescence detection schemes were implemented in tandem on a novel microfluidic device containing 39 parallel microchannels that were 500 μm tall, 250 μm wide, and 2.54 cm long with covalently tethered antibodies that was engineered for high-throughput high-volume sample processing. The devices were produced via a combination of high precision micromilling and hot embossing. Mass transfer limitations were found in conventional microsystems and were minimized due to higher surface area to volume ratios that exceeded those possessed by conventional microdevices and capillaries. Until now, these assays were limited to maximum total volume flow rates of ~1 mL/min due in part to kinetics and high head pressures of single microchannels. In the design demonstrated here, highly parallelized microchannels afforded up to a 100-fold increase in total volume flow rate while maintaining favorable kinetic constraints for efficient antigen-antibody interaction. The assay employed total volume throughput of up to 6 mL/min while yielding signal-to-noise ratios of >15 in all cases. In addition to samples being processed up to 60 times faster than in conventional displacement-based immunoassays, the current system was capable of quantitating 0.01 ng/mL TNT samples without implementing offline preconcentration, thereby, demonstrating the ability to improve sensitivity by as much as 2 orders of magnitude while decreasing total analysis times up to 60-fold.