In this work, a simple and low cost flow injection colorimetric system has been developed for fast screening determination of paraquat in natural water. A small LED-LDR colorimeter was fabricated to be used as a detector instead of a commercial spectrophotometer. The study of interferences shows less effect of matrix of natural water which is in agreement with a good percent recovery in spiking of paraquat into water samples. The proposed system provided sample throughput of 40 injections h−1 and low reagent consumption. Hence it is interesting to be used as an alternative method for determination of paraquat in water. With the cation exchange column preconcentration system, the lower limit of detection was achieved.