•We evaluated the uncertainty in mass measurements of four electronic configurations in lysimeter.•Uncertainty in excitation and acquisition by datalogger increase the system general uncertainty.•Periodic calibrations are necessary to compensate systematic errors due the damage by use.•Only regression analysis is not sufficient to evaluate weighing lysimeters.•Errors and uncertainties were attenuate due the use of indicator module in the Measurement System. The determination of measurement reliability in weighing lysimeters via error analysis is essential for scientific research and irrigation management. The objective of this study was to evaluate four different weight measuring systems (MSs) applied to load cell weighing lysimeters and compare the results with the expected uncertainty values obtained from data provided by manufacturers. A weighing lysimeter with an area of 0.385 m2 and a volume of 0.289 m3 was used, installed on three load cells. In MS1, the load cells were connected to a junction box and the box to a weighing indicator module in a six-wire configuration. In MS2, a four-wire connection was used between the junction box and a datalogger, whereas in MS3, there was a six-wire connection. For MS4, the connection between the load cells and datalogger was direct. The uncertainties of the measurement systems were determined from the calibration results. MS1 presented the lowest measurement errors and uncertainties, resulting in performance superior to those of the other MSs. After MS1, the best performances were obtained by MS2 and MS3, and MS4 presented the worst performance. The effect of the signal measurement uncertainties and the excitation by the datalogger had the greatest effects on the overall uncertainty of the system compared with the influence of temperature on the load cells. The measurement system may be selected according to the technical data supplied by the manufacturer; however, periodic calibration of the effective measuring range is necessary to verify and compensate for systematic errors, which are accentuated during the operation time.