With the growing interest in a circular economy, bio-based waste has become an important secondary raw material. Bio-concretes made with a cementitious matrix and plant waste-based aggregates have been the subject of increasing research in recent years. However, due to their high-water absorption capacity, the long-term durability of these materials remains uncertain. This study aims to experimentally and numerically investigate the capillary water transport behavior in partially saturated wood bio-concretes (WBC) and bamboo bio-concretes (BBC). The bio-concretes were produced with bio-aggregates contents of 25%, 35%, and 45% (by volume), and a cementitious matrix composed of cement, metakaolin and fly ash. In addition to capillary water absorption tests, bulk density, open porosity, total water absorption, and mechanical strengths were evaluated. A non-linear finite-element-based (FEM) model was employed to simulate the capillary transport phenomenon in bio-concretes by adopting a modified form of Darcy’s law. Experimental results indicate that wood bio-concrete exhibits a greater water absorption capacity, attributed to its higher porosity. Furthermore, inverse calibration results provide deeper insights into how the content and type of bio-aggregates influence the Raleigh-Ritz pore size distribution. Numerical results, which closely align with the experimental data, demonstrated that bio-concretes with higher Raleigh-Ritz parameter values generally exhibit lower capillary permeability performance.