The presence of toxic chemicals in water, including heavy metals like mercury and lead, organic pollutants such as pesticides, and industrial chemicals from runoff and discharges, poses critical public health and environmental risks leading to severe health issues and ecosystem damage; education plays a crucial role in mitigating these effects by enhancing awareness, promoting sustainable practices, and integrating environmental science into curricula to empower individuals to address and advocate for effective solutions to water pollution. However, the educational transformation should be accompanied with a technical process which can be eventually transferred to society to empower environmental education. In this study, carbonaceous material derived from Haematoxylum campechianum (CM-HC) was utilized for removing 3-nitrophenol (3-Nph) from aqueous solutions. The novelty of this research utilizes Haematoxylum campechianum bark and coconut shell, abundant agricultural wastes in Campeche, Mexico, for toxin removal, enhancing the adsorption process through artificial neural networks and genetic algorithms to optimize conditions and maximize the absorption efficiency. CM-HC’s surface morphology was analyzed using scanning electron microscopy (SEM/EDS), BET method, X-ray powder diffraction (XRD), and pHpzc. Kinetic models including pseudo-first-order (PFO), pseudo-second-order (PSO), and Elovich were applied to fit the data. Adsorption isotherms were determined at varying pH (3–8), adsorbent dosages (2–10 g/L), and temperatures (300.15–330.15 K), employing Langmuir, Freundlich, Temkin, and Redlich–Peterson models. PSO kinetics demonstrated a good fit (R2 > 0.98) for Ci = 50–100 mg/L, indicating a chemical adsorption mechanism. The Langmuir isotherm model exhibited the best fit, confirming chemical adsorption, with a maximum adsorption capacity (Qm) of 236.156 mg/g at T = 300.15 K, pH = 6, contact time = 3 h, and 2 g/L adsorbent dosage. Lower temperatures favored exothermic adsorption. Artificial neural networks (ANNs) were employed for deep learning, optimizing the predictive model for removal percentage. Correlation heat maps highlighted positive correlations between time, dosage, and removal percentage, emphasizing the impact of initial concentration on efficiency. ANN modeling, incorporating iterative optimization, yielded highly accurate predictions, aligned closely with experimental results. The study showcases the success of deep learning in optimizing adsorption processes, emphasizing the importance of diverse correlation algorithms for comprehensive insights into competitive adsorption dynamics. The 5-14-14-1 deep learning architecture, fine-tuned over 228 epochs, demonstrated strong performance with mean squared error (MSE) values of 4.07, 18.406, and 6.2122 for training, testing, and total datasets, respectively, and high R-squared values. Graphical analysis showed a solid linear correlation between experimental and simulated removal percentages, emphasizing the need to consider more than just testing data for optimization. Experimental validation confirmed a 98.77% removal efficiency, illustrating the effectiveness of combining deep learning with genetic algorithms, and highlighting the necessity of experimental trials to verify computational predictions. It is concluded that the carbonaceous material from Haematoxylum campechianum waste (CM-HC) is an effective, low-cost adsorbent for removing 3-nitrophenol from aqueous solutions, achieving optimal removal at pH 6 and 300.15 K with a maximum adsorption capacity of 236.156 mg/g, following Langmuir model and pseudo-second order kinetics. The validated ANN model offers a reliable tool for practical applications in environmental remediation, advancing both environmental science and educational innovation by integrating artificial neural networks and data science methodologies into student learning experiences.