In regions where microbial contamination of groundwater and surface water remains a significant public health concern, leading to around 505,000 annual deaths, there is an urgent need for accessible, cost-effective, and simple household water treatment solutions. This study investigated the feasibility of wood as a filtration system, with a focus on its ability to remove nanoparticles. The research underscores the remarkable potential of wood filters, particularly in radial and tangential directions, exhibiting superior particle removal capabilities (> 99%) due to extended residence time and intricate microstructures. The study reveals that wood type selection in this study, i.e., yellow poplar (Liriodendron tulipifera), European beech (Fagus sylvatica), Douglas fir (Pseudotsuga menziesii), and silver fir (Abies alba), plays a crucial role in filtration efficiency, with beech emerging as a high-performing option alongside silver fir. Importantly, the optimal range of size exclusion was identified (160–490 nm), aiding in designing wood filters for specific particle size reduction goals. Wood filters also show great potential for removing a broad range of microorganisms, i.e., bacteria and protozoa, as well as nanoplastics and microplastics, which could have profound implications for water treatment and environmental remediation. Furthermore, the study highlights the adsorption/diffusion process through the amorphous domains of the wood biopolymers, i.e., cellulose, hemicelluloses and lignin, enhanced by electrostatic interactions in the filtration efficiency for small organic molecules, providing valuable insights into filtration mechanisms.