Biochar is a stable carbon rich by-product synthesized through pyrolysis of plant and animal based biomass, and nano-biochar material has gained increasing attention due to its unique properties for environmental applications. In the present study, a simple cost-effective method for the synthesis of biochar nanoparticles through hydrothermally using agricultural residuals and by-products was developed. Both soybean straw and cattle manure were selected as the feedstock to produce the bulk-biochar. The synthesis procedure involved the digestion of the bulk-biochar with concentrated nitric acid and sulfuric acid in a high pressure condition using a hydrothermal reactor. The suspension was isolated using vacuum filtration with 0.22-μm membrane followed by drying at 65 °C in an oven. Scanning electron microscopy results revealed that both of the biochars had a well-developed porous structure following pyrolysis. Both transmission electron microscopy and the dynamic light scattering results of the hydrothermally treated biochar indicated that the soybean straw and cattle manure biochar nanodots had an average of 5-nm and 4-nm in size, respectively. Overall two raw materials produced 8.5–10% biochar nanodots. The present method presents a simple, quick and cost-effective method for synthesis of biochar nanodots. The method provided a useful tool discovering the applicability biochar nanodots for environmental applications.