A hyphenated sequential injection ion chromatography–flow injection analysis (SIIC–FIA) system is proposed for post column derivatization capable of using murexide, an unstable but commonly available reagent, for the determination of calcium and magnesium in a mixture. A short ion exchange column was modified from a 4.6 mm × 10 mm C18 monolithic guard column. Calcium/magnesium mixture and murexide were used as model analytes and derivatizing agent, respectively. The FIA post column allows the use of unstable chromogenic reagents. The continuous flow of liquid also helped to stabilize the signal baseline during detection. A single concentration based calibration graph was demonstrated. The system requires low volumes of standard/sample (5–50 µL) and mobile phase (4.50 mL), and offers sample throughput at 8 h−1 without the need for long column calibration. Detection limits were 0.5 and 0.1 µg for Ca2+ and Mg2+, respectively. Working ranges were 1–5 µg Ca2+ and 0.2–1 µg Mg2+. Analyses of well and drinking water samples were demonstrated and validated with the standard complexometric titration.