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.