A cost-effective, automated and portable IC has been developed for in-situ analysis of nitrite and nitrate in natural waters. The system employed 3D printed pumps for eluent delivery and a deep-UV LED based optical detector. Isocratic separation and selective detection of nitrite and nitrate was achieved in under 3 min. The total weight of the analyser was ~11 kg, and included electronics along with a sample intake system for automated analysis. Linear calibration ranges were generated using different sample injection loops. Using a 150 μL loop, an analytical range (0.05–30 mg L−1 NO2−, 0.10–75 mg L−1 NO3−) suitable for freshwater analysis was generated, while using a 10 μL loop an analytical range (0.30–100 mg L−1 NO2−, 2.5–500 mg L−1 NO3−) suitable for effluent and domestic wastewater analysis was achieved. Chromatographic repeatability demonstrated by the system is graphically presented and RSD values of <4% were obtained in terms of peak area and retention time over 82 sequential runs. The system was deployed in-situ at multiple sites for varying deployment periods analysing septic tank water, effluent from a waste water treatment plant and stream water. The data generated by the in-situ system were comparable to grab sample data generated by accredited laboratory instrumentation.