An online separation and preconcentration method, employing a lab-on-valve system using solid phase extraction, followed by inductively coupled plasma tandem mass spectrometry (ICP-MS/MS), was developed for the analysis of 90Sr. The 90Sr was separated from 90Zr, an isobaric interference present at high concentrations in many samples, and other matrix components using a dual-column setup (Eichrom DGA-B and Sr resins). Any remaining 90Zr was then chemically resolved from the 90Sr in the ICP-MS/MS using O2 and H2 reaction gases. The system requires small sample volumes (10 mL), minimal sample preparation compared to traditional radiometric and other MS techniques and has a processing time of 22 min per sample. Based on a 10 mL sample size, the system limit of detection, limit of quantification and method detection limit (MDL) were 0.47 Bq L−1 (0.09 pg L−1), 1.57 Bq L−1 (0.32 pg L−1) and 1.79 Bq L−1 (0.34 pg L−1), respectively. The robustness of the system and suitability for use in various sample matrices was demonstrated using spiked lake water, spiked groundwater, spiked seawater and radioactive water samples. Recovery of the IAEA 2018 Proficiency Test Exercise water sample (n = 5) was 99% with an RSD of 11.9%. The method thus provides a powerful tool for the rapid analysis of low levels of 90Sr in various water/wastewater samples. Display omitted •Automated separation of 90Sr from various complex matrices.•Preconcentration of 90Sr from sample volume of 10 mL followed by online measurement by ICP-QQQ-MS.•Accurate measurement of 90Sr in addition to analysis time of only 22 min per sample and low detection limit.•Suitable for emergencies requiring rapid response and for government agencies/industries needing to monitor aquatic systems.