The black-odor water body restoration is an unfinished business in protecting and maintaining the ecological functions of natural water systems in China. Magnetic coagulation (MC) had found a vast application prospect for its high-efficient separation. In this work, the performance of MC was analyzed to explore its role in natural water protection, with a focus on identification and removal mechanisms of the dissolved organic matters (DOM) by absorption and fluorescence spectroscopy in terms of the spectroscopic indices, two-dimensional correlation spectroscopy (2D-COS), and parallel factor analysis (PARAFAC) methods. MC presented an excellent performance for suspended and colloidal matters, phosphorus, and DOMs, and showed high adaptability in pollution interception and water restoration. Tryptophan-like, tyrosine-like, and humics were identified as the key components in the wastewater, which were mainly recently produced or microbial-derived. The targeted pollutants were DOMs with high molecular weight, hydrophobicity, polarity, and aromaticity for the high affinity with the hydrolyzed Al species. Polyaluminum chloride (PAC) was the key in dissolved pollutants removal, while the mix stage is crucial for DOMs with low MW or humic-like substances as PAM facilitated the flocs formation and the absorption process. However, the residual PAM and the redissolved DOMs from the recycled magnetic seeds also act as the DOM source. This work identified the DOM composition and removal mechanism in MC, which would promote its application in natural water protection.