This study investigated a novel agricultural low-cost bio-waste biochar derived from wood apple fruit shell waste via the pyrolysis method, which is modified by ball milling and utilized to remove toxic phenol and chlorophenols (4-CPh and 2,4-DCPh) from contaminated aqueous media. The ball-milled wood apple fruit shell waste biochar (WAS-BC) sorbent was systematically analyzed by BET, CHN, and FTIR as well as particle size, SEM-EDS, XPS and TGA studies. The sorption equilibrium and kinetic studies exhibit that the sorption capacity was greater than 75% within the first 45 min of agitation at pH 6.0. The uptake capacity of 2,4-DCPh onto WAS-BC was greater than those of 4-CPh and phenol. Equilibrium results were consistent with the Langmuir isotherm model, while the kinetic data were best represented by the Elovich and pseudo-second-order model. The maximum uptake of phenol, 4-CPh, and 2,4-DCPh was 102.71, 172.24, and 226.55 mg/g, respectively, at 30 ± 1 °C. Thus, this study demonstrates that WAS-BC is an efficient, low-cost sorbent that can be used for the elimination of phenol and chlorophenol compounds from polluted wastewater.