The Naval Research Laboratory has developed an array-based biosensor system capable of detecting multiple pathogenic and toxic species in complex matrices. Sandwich fluoroimmunoassays are performed on the surface of a patterned microscope slide that acts as an optical waveguide. Fluorescence from immunocomplexes formed on the slide surface is excited using the evanescent field, an electromagnetic component of light, and the pattern of fluorescence is imaged using a charge-coupled device camera. Using the evanescent wave for excitation allows real-time imaging. Alternatively, a confocal scanner can also be used to detect and quantify fluorescent spots. A method for immobilizing capture antibodies, performing assays, and detecting bound targets is presented.