The MR-linac is a hybrid MRI radiotherapy system allowing dose delivery in a 1.5 T magnetic field. This paper presents the design and performance of a prototype MR-linac compatible scanning water phantom. Since a scanning water phantom requires dose detectors, the performance air-filled ionization chambers in the magnetic field was characterized. We have found that the linearity and reproducibility of an ionization chamber are unaffected by the magnetic field. Also, moving the ionization chambers in a magnetic field during irradiation does not affect the dose response. When scanning in-plane profiles, the change in irradiation orientation can influence the ionization chamber dose response by up to 0.4%. However this effect can be eliminated by rotating the ionization chamber by 90° before measuring the in-plane profile. The performance of the total scanning water phantom was validated at a clinical setup in a 0 T magnetic field. There was no significant difference between the dose profiles measured with a standard clinical scanning water phantom and the profiles measured with the MR-linac compatible scanning water phantom. The performance of the MR-linac scanning water phantom in the MR-linac was validated using Gafchromic EBT2 film. There was no significant difference in dose profiles between the MR-linac scanning water phantom and the radiochromic film. These results indicate that automated scanning water phantom measurements using ionization chamber detectors are possible in the MR-linac.