The aim of this work is to evaluate the application of NiFe2O4 nanoparticles with spinel structures as the basis of catalysts for the purification of aqueous media from pollutants such as manganese and arsenic. The interest in these catalysts is due to their ease of production and high absorption efficiency, which, together with their magnetic properties, allow the use of nanoparticles for a long time. The sol–gel method, followed by thermal annealing of the samples at different temperatures, was proposed as a method for the synthesis of spinel nanoparticles. The choice of the annealing temperature range of 200–1000 °C is caused by the possibility of estimating changes in the structural properties and the degree of nanoparticles crystallinity. During the study of structural changes in nanoparticles depending on the annealing temperature, it was found that in the temperature range of 200–800 °C, there is an ordering of structural parameters, while for samples obtained at annealing temperatures above 800 °C, there is a partial disorder caused by the agglomeration of nanoparticles with a subsequent increase in their size. According to the results of the studies on the purification of aqueous media from pollutants, it was found that the greatest absorption efficiency belongs to nanoparticles annealed at 500–700 °C, with the purification efficiency of 70–85%, depending on the type of pollutant. The results obtained from the use of nanoparticles as catalysts for the purification of aqueous media show great prospects for their further application on an industrial scale.