A lithographic apparatus comprising an object table which carries an object. The lithographic apparatus may further comprise at least one sensor as part of a measurement system to measure a characteristic of the object table, the environment surrounding the lithographic apparatus or another component of the lithographic apparatus. The measured characteristic may be used to estimate the deformation of the object due to varying loads during operation of the lithographic apparatus, for example varying loads induced by a two-phase flow in a channel formed within the object table. Additionally, or alternatively, the lithographic apparatus comprises a predictor to estimate the deformation of the object based on a model. The positioning of the object table carrying the object can be controlled based on the estimated deformation. The positioning of a projection beam, used to pattern a substrate, can be controlled relative to the object, to alter the position of the pattern and/or the projection beam on the substrate, based on the estimated deformation.