Ferrihydrite is a mineral that exists in a nanoscale form. At the antiferromagnetic ordering of the magnetic moments of iron atoms, it exhibits, due to the uncompensated magnetic moment of its nanoparticles, the magnetic properties very similar to those of ferro-and ferrimagnetic nanoparticles. In this study, we investigate the ferrihydrite nanoparticles that are a co-product of the cultivation of bacteria. The obtained biogenic sample is an aggregate of biogenic nanoparticles with an average size of ~2 nm coated with a polysaccharide shell, which excludes contact magnetic interactions between particles. The features caused by the surface effects and the inhomogeneous structure of ferrihydrite have been examined in the temperature range of 4-300 K using Mössbauer spectroscopy and magnetometry. Based on the data obtained, the superparamagnetic blocking processes have been identified. The dominating contribution of the surface magnetic anisotropy to these processes has been established. This surface effect is caused by the inhomogeneous structure of ferrihydrite nanoparticles, which is confirmed by the Mössbauer spectroscopy data showing the existence of different states of iron nuclei. A core-shell structural model of ferrihydrite particles has been proposed. The particle core is well-crystallized, while the surface layer is loose and contains a greater number of defects. It has been found that the size of the dense core depends on the particle size; the critical value is d ~ 2 nm and the particles with a smaller diameter have no dense core. The results obtained reveal inhomogeneities of the crystal structure in ferrihydrite nanoparticles, which affect the magnetic properties of the investigated materials.