Femtosecond laser oscillator systems with low pulse energy (< 1 μJ) and high repetition rate (MHz) are increasingly used for precise, fast and safe eye surgery. Therefore, the laser tissue interaction process is of great interest to optimize and improve established and future surgical protocols. Besides, using faster laser systems leads to unintended self-induced interaction effects, where a femtosecond laser pulse modifies the vicinity in the material in such a way that the focus of following laser pulses is changed. We used a femtosecond oscillator laser system with high repetition rate and 66 nJ pulse energy to produce photodisruption in water. Water was used as phantom material for ocular tissue, because tissue mainly consists of water. A custom made digital-holographic system was used to measure the temporal material modification from picoseconds until seconds after occurrence of the photodisruption. For illumination of the sample we used either a continuously light source or the femtosecond laser pulse itself in a pump-probe configuration. The holographic system provides quantitative data of phase difference Δφ for the full field of view of several tenth of micrometers. Phase difference is equivalent to the laser induced change in the material’s refractive index which can alter focusing conditions of following laser pulses and might impair surgical outcome. We obtained the largest change in Δφ during the first picoseconds, followed by a slow relaxation of Δφ within some milliseconds. The results of time resolved measurements of the laser induced material modification will help to optimize scanning schemes in ocular surgery.