This paper describes two prototypes of an on-site Early Warning Water Quality Monitoring System (EWWQMS) for pesticide quantification in natural waters. As many pesticides are non-fluorescent, the EWWQMS setup uses UV photoconversion to form highly fluorescent photoproducts. To enhance sensitivity, the two prototypes use micellar-enhanced fluorescence with surfactant (cetyl trimethyl ammonium chloride) in aqueous solution. To improve specificity, four UV LEDs at different wavelengths then excite the fluorescent photoproducts. The EWWQMS prototypes also employ UV absorption for quantification of non-photosensitive pesticides. The first prototype detects the pesticides via a diode array spectrometer. The second system is developed with higher resolution spectrometer and an intensified CCD camera detection to improve the sensitivity of the method. These experimental set-ups are described, explained and tested. Analytical applications were carried out online in CTAC aqueous solution, for the determination of isoproturon, flufenoxuron and profenofos. The calibration curves obtained are linear over one order of magnitude, and the detection limits are in the ng mL−1 range. The analytical performances of these new methods are good compared with other published classical micellar enhanced photo-induced fluorescence methods for the determination of pesticides in aqueous solutions. Our results show that these EWWQMS prototypes can be used as a warning system to protect against pesticide contamination exceeding the threshold of treatment capabilities at industrial facilities using natural waters.