Ecofriendly hydrothermal reduction of graphene oxide is widely used for producing hydrogels and aerogels, but it yields partly reduced graphene oxide (prGO) containing oxygen groups and some number of paramagnetic centers (PCs). In order to identify structural changes introduced by the reduction process, these PCs are studied by electron spin echo spectroscopy in the temperature range of 5–160 K. Two types of PCs with different spin–lattice (T1) and phase memory (Tm) relaxation times observed below 20 K result from a nonuniform distribution of magnetic defects. Above 20 K, only the PCs with the shorter T1 and Tm persist. Temperature dependences of T1 and the distribution of T1 for each type of the PCs reveal lattice distortions around the PCs and structural disorder in prGO. The unusually strong temperature dependence of the spin echo intensity is explained by the localization of conduction electrons. The localization is destroyed at high temperature, and exchange interactions decrease the number of the observed PCs. Every such PC is created by the sp3 defect induced by hydrogen covalently bonded to graphene. The obtained results indicate that the hydrothermal reduction is accompanied by partial hydrogenation of graphene. The presence of such hydrogen atoms is confirmed by infrared spectroscopy.