The aim of this work was to compare the performance of biochar from various food processing wastes of different origin for the removal of different nutrients from water. Eggshells (EGS), rice husk (RH), and coffee biochars were pyrolyzed at 400 and 800 °C and were examined for the removal of phosphates, nitrates, and ammonia nitrogen. The raw materials were also modified with magnesium chloride in order to investigate their sorption behavior. The highest sorption capacity (qmax) for phosphates and ammonium was observed with EGS pyrolyzed at 800 °C and was 11.45 mg PO43−-P/g and 11.59 mg NH3-N/g, while the highest nitrates sorption capacity was observed with the magnesium-modified RH pyrolyzed at 800 °C (5.24 mg NO3−-N). The modified EGS biochars pyrolyzed at 800 °C had almost the half the sorption capacity for phosphates and nitrates compared to the unmodified materials. The modification of RH pyrolyzed at 800 °C resulted in higher sorption capacity by 34 and 158% for phosphates and ammonium, respectively. The coffee raw and modified biochars were less efficient in nutrient removal compared to the other materials. The specific surface area values of the biochars examined is not a decisive factor for nutrient sorption. The reaction between magnesium and calcium (for the eggshell samples) ions with phosphates is responsible for the higher sorption efficiency. On the other hand, the presence of magnesium and calcium ions has a detrimental effect on the sorption of NH3-N.