A batch experiment was conducted to examine the behavior of nitrate, organic ligands, and phosphate in the co-presence of biochar and three common low-molecular-weight organic acids (LMWOAs). The results show that citrate, oxalate, and malate ions competed with nitrate ion for the available adsorption sites on the biochar surfaces. The removal rate of LMWOA ligands by the biochar via adsorption grew with increasing solution pH. The adsorbed divalent organic ligands created negatively charged sites to allow binding of cationic metal nitrate complexes. A higher degree of biochar surface protonation does not necessarily enhance nitrate adsorption. More acidic conditions formed under a higher dose of LMWOAs tended to make organic ligands predominantly in monovalent forms and failed to create negatively charged sites to bind cationic metal nitrate complexes. This could adversely affect nitrate removal efficiency in the investigated systems. LMWOAs caused significant release of phosphate from the biochar. The phosphate in the malic acid treatment tended to decrease over time, while the opposite was observed in the citric- and oxalic-acid treatments. This was caused by re-immobilization of phosphate in the former due to the marked increase in solution pH over time.