The surface states of silicon nanocrystals (Si-ncs) considerably affect quantum confinement effects and may determinate final nanocrystals properties. Colloidally dispersed Si-ncs offer larger freedom for surface modification compared to common plasma enhanced chemical vapor deposition or epitaxial synthesis in a solid matrix. The Si-ncs fabrication and elaboration in water by pulsed laser processing is an attractive alternative for controlling and engineering of nanocrystal surface by environmentally compatible way. We report on the possibility of direct silicon surface ablation and Si-ncs fabrication by nanosecond pulsed laser fragmentation of electrochemically etched Si micrograins and by laser ablation of crystalline silicon target immersed in de-ionized water. Two nanosecond pulsed lasers (Nd:YAG, and excimer KrF) are successfully employed to assure fragmentation and ablation in order to produce silicon nanoparticles. Contrary to the fragmentation process, which is more efficient under Nd:YAG irradiation, the laser ablation by both lasers led to the fabrication of fine and room temperature photoluminescent Si-ncs. The processing that has natural compatibility with the environment and advanced state of fabrication technologies may imply new possibilities and applications.