Calibration of stream gauging stations involves water velocity measurements at various water levels to obtain discharge and to determine the rating curve. This process is laborious, often logistically challenging, or even impossible for streams that are only accessible at low flow. Here, we present an alternative method to obtain mean stream velocity by matching temperature variation patterns measured at two positions in the stream. Such water temperature variations are caused by snow melt or rainfall events and serve as natural tracers. The method is successfully applied to a karst cave stream that is only accessible at lowest flow. The installed high‐precision data loggers provide sufficient data to obtain a relationship between water depth and mean velocity. The approximate rating curve, based on reach mean channel width, agrees well with results from dye tracer experiments. This cave stream shows the typical features of a steep step‐pool stream such as a power law relation between mean velocity and discharge.