Raman scattering in ensembles of silicon (Si) nanocrystals (NCs), which were prepared by differed methods and then stored in an aqueous medium, was studied to reveal features of the Si NC dissolution process. Arrays of crystalline Si nanowires, mesoporous Si nanoparticles and spherical Si NCs have been analyzed after exposure in water during dialysis for elimination of the dissolution products from the medium. According to the one-phonon Raman spectroscopy the Si nanowires with cross-section size of the order of 100 nm were resistant to the dissolution process both in water and physiological saline for 2 weeks at least. The storage of mesoporous Si nanoparticles in water for 1 day resulted in a strong decrease of the Raman intensity and a low energy shift of the Raman spectrum, which was explained by size reduction of Si NCs below 10 nm. Si NCs with the initial size distribution from 5 to 100 nm after exposure in water during 24 hours revealed a decrease in the contribution of small NCs that narrowed the size distribution. The obtained results can be used in order to choose appropriate type of Si NPs for biomedical applications.