This work describes a methodology that can be used to achieve on-site analysis of paraquat in water samples by using a miniaturized portable photometer consisting of a couple of light-emitting diodes (LEDs). Paraquat produces a colored radical via a redox reaction with sodium dithionite, which is unstable against oxygen in solution. The steps taken to stabilize the reagent solution included control of the pH and the addition of organic solvents, but the most effective was the formation of an oil layer. Together, these steps stabilized the reagent solution for two days. An increase in the duration of reagent stability, however, is necessary in order to transport the reagent for on-site applications in remote locales. For the time being, an excess amount of solid sodium dithionite can be added directly to sample solutions because the unreacted dithionite shows no influence on absorbance of the paraquat radical. Orange LEDs with a maximum emission wavelength of 609 nm were employed in the portable photometer to measure the absorbance of paraquat radical produced by a redox reaction that has an absorption maximum of 603 nm. The developed photometer showed excellent performance with a linear range of from 2.0 mg L−1 to 40.0 mg L−1 and a linear regression (r2 = 1). The limits of detection and quantification were 0.5 mg L−1 and 1.5 mg L−1, respectively, intra-day precision (n = 3) and inter-day precision (n = 5) were both less than 5%, and accuracy based on the percentage of sample recovery ranged from 89 ± 0 to 105 ± 0% (n = 3). The proposed method was applied to the analysis of paraquat in water samples taken from rice fields. The results showed no paraquat in all thirteen samples, which could have been due to strong adsorption of paraquat by soil particles and/or to complications with the sampling conditions. To confirm the adsorption onto soil of paraquat contained in water, we constructed an artificial rice field where water containing paraquat was impounded above the soil layer. The results showed that paraquat in water gradually decreased within three days and could be measured in the soil on the fourth day. These results were confirmed by HPLC analysis, which underscores the utility of this portable photometer for the on-site monitoring of paraquat in water samples.