Strontium-90 (90Sr) is the major long-lived radionuclide derived from the Chernobyl accident, and is still being detected in the heavily contaminated catchments of the Chernobyl Exclusion Zone. This study examines the long-term decrease in the dissolved-phase 90Sr concentration and the concentration–discharge (90Sr-Q) relationship in stream water since the accident. We show that the slow decline in 90Sr follows a double-exponential function, and that there is a clear relationship between 90Sr and Q. This study is the first to reveal that the log(90Sr)-log(Q) slope has been gradually decreasing since the accident. This trend persists after decay correction. Thus, it is not caused by the physical decay of 90Sr and environmental diffusion, but implies that the concentration formation processes in stream water have been changing over a long period. We propose a hydrochemical model to explain the time-dependency of the 90Sr-Q relationship. This paper presents a mathematical implementation of the new concept and describes the model assumptions. Our model accurately represents both the long-term 90Sr trend in stream water and the time-dependency of the 90Sr-Q relationship. Although this paper considers a small catchment in Chernobyl, the conceptual model is shown to be applicable to other accidental releases of radionuclides.