A fluid analyzer includes an optical source and an optical detector defining an optical beam path through an interrogation region of a fluid flow cell. Motion control devices determine position of the interrogation region. Flow-control devices conduct analyte and reference fluids and manipulate fluid flow in response to control signals to position a fluid boundary across the interrogation region. A controller (1) generates a time-varying motion modulation signal to move the interrogation region across the fluid boundary, (2) samples an output signal from the optical detector at one time in which the interrogation region contains more analyte fluid than reference fluid and at a time at which the interrogation region contains more reference fluid than analyte fluid, thereby generating corresponding output signal samples, and (3) determines from the output signal samples a measurement value indicative of an optically measured characteristic of the analyte fluid.