Method for controlling a liquid chromatography system comprising a system pump and a column in fluid communication with the system pump by a fluid flow path, the method comprising the steps: registering the system pressure at a flow path position close to the system pump, controlling the operation of the system pump in response to the registered system pressure, estimating a pre-column pressure based on the registered system pressure, the characteristics of the flow path, and the viscosity and flow-rate of the liquid in the system, and controlling the operation of the system pump in response to the estimated pre-column pressure.