Abstract Background Prior work demonstrated that free water in the posterior substantia nigra (SN) was elevated in Parkinson's disease (PD) compared to healthy controls (HC) across single- and multi-site cohorts, and increased over 1 year in Parkinson's disease but not in relation with the iron deposition in SN with the relaxometry T2*. Objectives The main objective of the present study was to evaluate changes in the SN using relaxometry T2*, single- and bi-tensor models of diffusion magnetic resonance imaging between PD patients and HC. Methods 39 subjects participated in this study, including 21 HCs and 18 PD patients, in moderate stage (7 years), whose data were collected at two visits separated by approximately 2 years, underwent 3-T MRI comprising: T2*-weighted, T1-weighted and diffusion tensor imaging (DTI) scans. Relaxometry T2*, bi-tensor free water (FW), free-water-corrected fractional anisotropy, free-water-corrected mean diffusivity, single-tensor fractional anisotropy, and single-tensor mean diffusivity were computed for the anterior, posterior and whole substantia nigra. Results In the anterior SN, relaxometry T2* values were greater for PD patients than HCs. In the posterior SN, free water, single- and bi-tensor mean diffusivity values were greater for PD patients than HCs. No significant change were found over time in FW/MD/R2* maps for PD patients with moderate stage. Conclusion The specific increase of R2* in the anterior SN concomitant with the specific increase of FW in posterior SN suggests a complementary aspect of the two parameters and, perhaps, different underlying pathophysiological processes.