Chemical weathering of volcanic rocks in warm and humid climates contributes disproportionately to global solute fluxes. Geochemical signatures of solutes and solids formed during this process can help quantify and reconstruct weathering intensity in the past. Here, we measured silicon (Si) and germanium (Ge) isotope ratios of the soils, clays, and fluids from a tropical lowland rainforest in Costa Rica. The bulk topsoil is intensely weathered and isotopically light (mean ± 1σ: δ30Si = −2.1 ± 0.3‰, δ74Ge = −0.13 ± 0.12‰) compared to the parent rock (δ30Si = −0.11 ± 0.05‰, δ74Ge = 0.59 ± 0.07‰). Neoforming clays have even lower values (δ30Si = −2.5 ± 0.2‰, δ74Ge = −0.16 ± 0.09‰), demonstrating a whole‐system isotopic shift in extremely weathered systems. The lowland streams represent mixing of dilute local fluids (δ30Si = 0.2 − 0.6‰, δ74Ge = 2.2 − 2.6‰) with solute‐rich interbasin groundwater (δ30Si = 1.0 ± 0.2‰, δ74Ge = 4.0‰). Using a Ge‐Si isotope mass balance model, we calculate that 91 ± 9% of Ge released via weathering of lowland soils is sequestered by neoforming clays, 9 ± 9% by vegetation, and only 0.2 ± 0.2% remains dissolved. Vegetation plays an important role in the Si cycle, directly sequestering 39 ± 14% of released Si and enhancing clay neoformation in surface soils via the addition of amorphous phytolith silica. Globally, volcanic soil δ74Ge closely tracks the depletion of Ge by chemical weathering (τGe), whereas δ30Si and Ge/Si both reflect the loss of Si (τSi). Because of the different chemical mobilities of Ge and Si, a δ74Ge‐δ30Si multiproxy system is sensitive to a wider range of weathering intensities than each isotopic system in isolation.