Soil degradation and water stress in Costa Rica challenge the production of highly sensitive crops. This work is aimed at evaluating the physical and chemical changes in sandy loam (SL) and a silt loam (SiL) soil when amended with bamboo biochar while estimating the enhancement of tomato productivity. Biochar, obtained from Guadua Angustifolia bamboo feedstock, was mixed into sieved bulk soil substrate from the topsoil, from Andosol and Umbrisol groups, at application rates of 1, 2.5, and 5% (dry mass). Physicochemical and morphological properties of biochar such as pH, hydrophobicity, scanning electron microscopy images, helium picnometry, specific surface area by the Brunauer–Emmett–Teller (BET) method, CHNS, and ash content were determined. Soil hydrophobicity, acidity, electrical conductivity, cation exchange capacity and water retention, available water content, and air capacity were analyzed for the amended soils. Tomato yield was quantified after a harvest period of two months. The admixture of biochar did not significantly increase soil cation exchange capacity but increased water retention in the range of available water content. Class A (>200 g) tomato yield increased 350% in the SL and 151% in the SiL. Class B (100–200 g) tomato yields increased 27% in the SL but decreased about 30% in the SiL. Tomato yield response seems attributable to variation of water retention capacity, available water content, and air capacity. These results support the use of adapted water management strategies for tomato production based on soil physical changes of biochar.