The textile industry has more than doubled from 2020 to 2024, disrupting ecosystems. Current remediation methods like coagulation-flocculation are energy-intensive and costly. Biodegradable hydrogels, with hydrophilic functional groups and porous structures, offer a sustainable alternative. This study optimized hydrogel-based dye remediation of Methylene blue (MB) and Methyl Orange (MO) using computational and experimental approaches. To predict the hydrogel-dye interactions at a molecular level, computational simulations (Avogadro, Auto Dock Vina, ORCA) screened 30 hydrogels based on their binding energies, identifying four promising hydrogels (beaded, emulsion templating, dual crosslinking, and CH/GG/CR). They were tested for physical properties, dye adsorption, dye desorption/reusability, surface charges, temperature stability, functional groups, and biotoxicity. A novel self-cleaning 3D-printed column was developed to enhance dye adsorption efficiency by minimizing clogging and enabling continuous operation with minimal human intervention. Statistical analysis was conducted using a one-way analysis of variance (ANOVA), followed by Tukey’s post hoc. The CH/GG/CR hydrogel achieved the highest efficiency(p<0.05), reducing MB and MO concentrations to 0.33 ppm and 0.64 ppm(p<0.05), respectively. Graphene oxide further enhanced adsorption, achieving reductions to 0.2 ppm (MB) and 0.4 ppm (MO); however, the additive of the CQD showed the best balance of efficiency and cost effectiveness. FTIR analysis confirmed the presence of key functional groups (OH, NH2−). Biotoxicity tests showed minimal effects. Reusability tests with HCl (MB) and NaOH (MO) were effective. This waste product is a concentrated dye solution which could be reused in industries to directly contribute to the circular water economy. Due to the material and cost constraints, some future studies should explore the scalability of these biodegradable hydrogels under varying flow rates and environmental conditions.