This study developed bio-based waterborne polyurethane (BWPU) dispersions containing lignin as a sustainable filler with castor oil (CO), polycaprolactone diol (PCL), or poly(trimethylene ether) glycol (PO3G). The effects of the polyol structure and the presence of lignin on the mechanical performance, thermal stability, water absorption, ethanol resistance, and UV-blocking capabilities of the resulting BWPU samples were evaluated. The results revealed that lignin affects the molecular packing and interchain interactions of CO-based BWPU, thus improving its tensile strength and thermal stability while reducing its water absorption and ethanol permeability. In the PCL-based BWPU, lignin had a minimal impact on water absorption and ethanol resistance but led to greater UV-blocking ability due to interactions between the semi-crystalline matrix of PCL and the aromatic structure of the lignin. In the PO3G-based BWPU, lignin disrupted the polymer network, increasing its water absorption and reducing its ethanol resistance but significantly improving its elongation and UV-shielding behavior. These results highlight the dual role of lignin as a sustainable reinforcing agent and functional additive in enhancing the properties of BWPU. By tailoring the polyol structure and optimizing lignin use, this study demonstrates a framework for the development of eco-friendly PU composites suitable for use as coatings, barriers, UV-shielding films, and packaging.