The error induced by susceptibility changes due to respiration in the measurement of CSF flow was investigated. Real-time dynamic B0 measurements and PCMRI images of 10 healthy subjects were acquired. A good agreement was found between both acquisitions. B0 amplitudes and temporal shifts with respect to respiration signals showed dependencies on echo times, temporal distances between phase contrast images and subjects. Resulting errors between 0.4 and 41 % in PCMRI images were shown in simulations. In conclusion, the present work demonstrates that B0 variations during respiration may have a confounding effect when estimating respiration dependent flow in CSF.