A sensor apparatus (300) for determining a position of a target (330) of a substrate (W) comprising, projection optics (315;321) configured to project a radiation beam (310) onto the substrate, collection optics (321) configured to collect measurement radiation (325) that has scattered from the target, a wavefront sensing system (335) configured to determine a pupil function variation of at least a portion (355) of the measurement radiation and output a signal (340) indicative thereof, and a measurement system (350) configured to receive the signal and to determine the position of the target in at least partial dependence on the collected measurement radiation and the determined pupil function variation of at least a portion of the measurement radiation.