Research on using biochar as an adsorbent of contaminants in aqueous matrices has gained significant relevance in recent years due to the surface chemistry and porous structure of biochar, which facilitate the retention of a wide range of pollutants. This study explores the adsorption performance of a novel biochar produced from agave bagasse—a readily available agro-industrial waste in Mexico—through low-temperature pyrolysis. The biochar was evaluated for its capacity to remove conventional water quality parameters (chemical oxygen demand (COD), nitrates (NO₃⁻), total nitrogen (TN), total phosphorus (TP), ammonium (NH₄⁺), turbidity, apparent color, and true color) from water samples collected from the polluted Bustillos Lagoon in Chihuahua, Mexico. Additionally, the removal of emerging pharmaceutical contaminants, specifically acetaminophen (Act) and diclofenac (Dfc), was assessed in synthetic aqueous solutions. Potentiometric titration analyses revealed a significant contribution of surface acidity in the adsorption of pharmaceutical derivatives, highlighting the relevance of functional groups retained during low-temperature pyrolysis. The biochar derived from agave bagasse (BBAF1) was tested in a fixed-bed column system and compared with two commercial activated carbons (CACCF2 and CVCF3). The BBAF1 biochar achieved average removal efficiencies ranging from 50% to 90% for all conventional parameters. In contrast, those of ACT and DFC were between 0.43 and 0.67 mg g⁻¹ (59–85%) and 0.34 and 0.62 mg g⁻¹ (37–79%), respectively, demonstrating their potential as an adsorbent material for improving water quality. This work supports the development of circular economic strategies by valorizing agricultural residues while offering an effective solution to environmental pollution challenges.