Boron-based nanoformulations look very promising for biomedical applications, including photo- and boron neutron capture therapies, but the fabrication of non-toxic water-dispersible boron (B) nanoparticles (NPs), which contain the highest boron atom concentration, is difficult using currently available chemical and plasma synthesis methods. Here, we demonstrate purely aqueous synthesis of clean boron NPs by methods of femtosecond laser ablation from a solid boron target in water, thus free of any toxic organic solvents, and characterize their properties. We show that despite highly oxidizing water ambience, the laser-ablative synthesis process follows an unusual scenario leading to the formation of elemental boron NPs together with boric acid (H3BO3) as an oxidation by-product, which acts to stabilize the elemental boron NPs dispersion. It was found that the formed NPs are spherical and composed of crystalline core covered by a thin sub-oxide shell, while their mean size is about 50 nm. We then demonstrate the purification of boron NPs from residual boric acid in deionized water, followed by their coating with polyethylene glycol to improve colloidal stability and biocompatibility. The synthesized NPs demonstrate low toxicity. They exhibit relatively strong absorption over a broad spectral range, in the NIR window of relative tissue transparency, promising their use as contrast agents for photoacoustic imaging and sensitizers of phototherapy, in addition to their promise for neutron capture therapy. This combined potential ability of generating imaging and therapy functionalities makes laser-synthesized B NPs a very promising multifunctional agent for biomedical applications.