A treatment planning system (106) for generating patient-specific treatment margins. The system (106) includes one or more processors (142). The processors (142) are programmed to receive a radiation treatment plan (RTP) for irradiating a target (122) over the course of one or more treatment fractions. The RTP including one or more treatment margins around the target (122) and a planned dose distribution for the target (122). The processors (142) are further programmed to receive motion data for at least one of the treatment fractions of the RTP from one or more target surrogates (124), calculate a motion-compensated dose distribution for the target (122) using the motion data and the planned dose distribution, compare the motion-compensated dose distribution to the planned dose distribution, and adjust the treatment margins based on dosimetric differences between the motion-compensated dose distribution and the planned dose distribution.