Forest is one of nature's most generous gifts to human beings, providing materials and shelters for all living beings with over 30% global land coverage. Apart from being sustainable, biodegradable, and renewable, wood is also extremely fascinating from the application aspect, with numerous advantages including hierarchical and macroporous structure, excellent mechanical performance, and versatile chemistry. The macroporous structure of wood is comprised of numerous long, partially aligned channels along the growth direction. This structure is suitable for a range of emerging applications, especially as a separation/membrane material. In this research, the potentiality of Gingko biloba (Gb) wood in the remediation of wastewater, contaminated with methylene blue (MB), a dye found in the industrial waters, was investigated. We report a macroporous, three-dimensional (3D) Gb-wood membrane decorated with palladium nanoparticles (Pd NPs) for efficient wastewater treatment. The efficiency of the Pd NPs/Gb-wood membrane to remove MB from a flowing aqueous solution was demonstrated. The wastewater treatment rate of the 3D Pd NPs/Gb-wood membrane can reach 0.5 L/min, with a high MB removal efficiency (>99.9%). The 3D Gb-wood macroporous membrane with partially aligned channels exhibits promising results for water treatment and is applicable for an even wider range of separation applications. In addition, the benefit of this 3D-wood membrane system for wastewater treatment was evaluated against the potential impacts on the environment and human health by employing the life-cycle assessment (LCA) approach. The LCA was carried out using the Gabi-education version with the gate-to-grave approach, including industrial wastewater, 3D-wood membrane, and electricity consumption using CML (Centrum VoorMilieukunde Leiden). From the LCA, it can be observed that wastewater filtration using this membrane exhibited a better environmental footprint due to the improved performance of the membrane in treating a higher volume of the permeate. Therefore, this filtration system had outweighed the additional environmental impact of the wastewater treatment process. The energy demand was identified as the main environmental hotspot in the LCA analysis. The analysis revealed that the energy source for electricity generation had a significant influence on the overall sustainability of this system. Additionally, the wood itself, a naturally abundant and eco-friendly material, presented zero environmental hazard to the environment during the filtration process. The experimental and environmental impact results indicate that Gb-wood can be employed as a natural and eco-friendly adsorbent material for the removal of waste from aqueous solutions.