To replace a pesticide immunoassay based on microtiter plates, we have developed a quantitative, competitive microarray immunoassay, which permits rapid and highly sensitive quantification of the dichlobenil degradation product 2,6-dichlorobenzamide (BAM), and the prominently used herbicide atrazine. The pesticide analysis is based on the competitive binding of fluorescence conjugated monoclonal antibodies (mAb) to their respective analytes. Lowest detection limits were calculated to 1 ng/l (5 pM) for BAM and 3 ng/l (10 pM) for atrazine. Corresponding IC(50) values were, 10 ng/l (50 pM) for BAM and 34 ng/l (160 pM) for atrazine, respectively. In comparison to the existing microtiter plate immunoassay, the microarray was found to be up to 20-fold more sensitive. Compared to the gas chromatography with mass spectroscopy (GCMS) analysis performed on more than 1000-fold concentrated samples, the microarray-based immunoassay was even 10-fold more sensitive using non-concentrated samples. Measuring both analytes simultaneously did not affect assay sensitivity compared to single analyte quantification. Besides a gain in sensitivity and the possibility of multiplex quantification, assay times and assay complexity were reduced drastically with the microarray platform compared to the microtiter plate immunoassay and GCMS, suggesting that the microarray based immunoassay is a viable method for measuring picomolar amounts of analytes, e.g. clinically relevant analytes.