Environmental considerations along with the technological challenges have led to search for green and energy-efficient processes for advanced nanostructured materials. In this study, nanobiochar was produced from pine wood biochar using a planetary ball mill. A central composite experimental design and response surface methodology was employed to optimize the ball milling parameters including time, rotational speed and ball to powder mass ratio to obtain nanoparticles in short time and at lower energy consumption. ANOVA results showed that the linear and quadratic effect estimates of time and the interaction effect of time and rotational speed were significant contributors to the size of particles during milling (p < 0.05). Based on the developed statistical model, the optimum conditions for obtaining the smallest particles, around 60 nm, were found to be 1.6 h, 575 rpm and 4.5 g/g. However, the size measurements indicated that particles had a great tendency to agglomerate. Further study showed that the conditioning of biochar at cryogenic temperatures prior to milling inhibits the agglomeration of nanoparticles which is essential in industrial processes. The adsorption test proved that the nanobiochar produced using green method is promising in the removal of micropollutants from aqueous media by removing up to 95% of carbamazepine from water. At the optimum milling parameters and conditioning for 24 h at −80 °C, nanobiochar with the average size of around 60 nm was obtained. The produced nanobiochar was characterized by Brunauer-Emmett-Teller (BET) gas porosimetry, scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). Also, physical and chemical properties, such as water holding capacity, organic matter, oxidation-reduction potential (ORP), elemental composition, polycyclic aromatic hydrocarbons (PAHs) and heavy metals were analyzed.