Abstract Histopathologic studies report higher concentrations of multiple sclerosis (MS) white matter (WM) lesions in watershed (ws) areas of the brain, suggesting that areas with relatively lower oxygen levels may be more vulnerable to disease. However, it is unknown at what point in the disease course lesion predilection for ws territories begins. Accordingly, we studied a cohort of people with newly diagnosed disease and asked whether (1) WM lesions disproportionally localize to ws-regions and (2) the degree of microstructural injury in ws-lesions is more severe. Fifty-four participants, i.e., 38 newly diagnosed people with MS, clinically isolated syndrome (CIS), or radiologically isolated syndrome (RIS), and 16 age- and sex-matched healthy controls (HCs) underwent brain magnetic resonance imaging (MRI). T1-weighted (T1-w) and T2-w fluid-attenuated inversion recovery (FLAIR) sequences, selective inversion recovery quantitative magnetization transfer (SIR-qMT) images, and the multi-compartment diffusion imaging with the spherical mean technique (SMT) were acquired. We computed the macromolecular-to-free pool size ratio (PSR), and the apparent axonal volume fraction (Vax) maps to indirectly estimate myelin and axonal integrity, respectively. We produced a flow territory atlas in each subject’s native T2-w FLAIR images using a T1-w MRI template in the Montreal Neurological Institute 152 space. Lesion location relative to the ws, non-watershed (nws), and mixed (m) brain vascular territories was annotated. The same process was performed on the T2-w FLAIR images of the HCs using 294 regions of interest (ROIs). Generalized linear mixed models for continuous outcomes were used to assess differences in size, PSR, and Vax between lesions/ROIs (in HCs) situated in different vascular territories. In patients, we assessed 758 T2-lesions and 356 chronic black holes (cBHs). Ws-territories had higher relative and absolute concentrations of T2-lesions (p≤0.041) and cBHs (p≤0.036) compared to either nws- or m-zones. T2-lesions in ws-areas also had lower PSR relative to T2-lesions in either nws- or m-zones (p=0.039). These results retained significance in the sub-cohort of people without vascular comorbidities or when accounting for periventricular lesions. In HCs, Vax was higher only in m-areas ROI compared to nws-ones (p=0.008). No differences in PSR were seen. We provide in vivo evidence that there is an association between arterial vascularization of the brain and MS-induced tissue injury as early as the time of disease diagnosis. Our findings underline the importance of oxygen delivery and healthy arterial vascularization to prevent lesion formation and foster a better outcome in MS.