PurposeThree‐dimensional (3D) dosimetry is a necessity to validate patient‐specific treatment plans in particle therapy as well as to facilitate the development of novel treatment modalities. Therefore, a vendor‐agnostic water phantom was developed and verified to measure high resolution 3D dose distributions.MethodsThe system was experimentally validated at the Marburger Ionenstrahl‐Therapiezentrum using two ionization chamber array detectors (PTW Octavius 1500XDR and 1000P) with 150.68 MeV proton and 285.35 MeV/u 12C beams. The dose distribution of several monoenergetic and complex scanned fields were measured with different step sizes to assess the reproducibility, absolute positioning accuracy, and general performance of the system.ResultsThe developed system was successfully validated and used to automatically measure high resolution 3D dose distributions. The reproducibility in depth was better than ±25 micron. The roll and tilt uncertainty of the detector was estimated to be smaller than ±3 mrad.ConclusionsThe presented system performed fully automated, high resolution 3D dosimetry, suitable for the validation of complex radiation fields in particle therapy. The measurement quality is comparable to commercially available systems.