Modern industrialization leads to the widespread discharge of pollutants, such as organic dyes and bacterial contamination, into water streams, necessitating efficient and sustainable treatment strategies. To address this challenge, we report the fabrication of biodegradable adsorbents for efficient adsorption of chemical pollutants while reducing the microbial load. Herein, kraft lignin (KL) is cross-linked with chitosan to produce highly porous spherical beads, while EDC/NHS ((N-ethyl-N′-(3-(dimethylamino)propyl)carbodiimide/hydroxysuccinimide) coupling chemistry enabled the formation of microporous sponges and alginate-integrated beads. Cross-linking with chitosan induced a surface charge reversal of lignin from negative (−37 mV) to positive (+51 mV), enhancing its affinity for anionic contaminants. The resulting materials exhibited promising adsorption capacity for an organic pollutant (methyl orange). Furthermore, the composites demonstrated efficient bacterial adsorption, achieving complete adsorption of E. coli (∼4 log reduction) using the lignin–chitosan sponge. These results highlight the potential of lignin–chitosan architectures as sustainable and multifunctional materials for advanced water purification.