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Abstract Lithium isotopes are used to trace weathering intensity, but little is known about the processes that fractionate them in highly weathered settings, where secondary minerals play a dominant role in weathering reactions. To help fill this gap in our knowledge of Li isotope systematics, we investigated Li isotope fractionation at an andesitic catchment in Puerto Rico, where the highest rates of silicate weathering on Earth have been documented. We found the lowest δ⁷Li values published to date for porewater (−27‰) and bulk regolith (−38‰), representing apparent fractionations relative to parent rock of −31‰ and −42‰, respectively. We also found δ⁷Li values that are lower in the exchangeable fraction than in the bulk regolith or porewater, the opposite than expected from secondary mineral precipitation. We interpret these large isotopic offsets and the unusual relationships between Li pools as resulting from two distinct weathering processes at different depths in the regolith. At the bedrock‐regolith transition (9.3–8.5 m depth), secondary mineral precipitation preferentially retains the lighter⁶Li isotope. These minerals then dissolve further up the profile, leaching⁶Li from the bulk solid, with a total variation of about +50‰withinthe profile, attributable primarily to clay dissolution. Importantly, streamwater δ⁷Li (about +35‰) is divorced entirely from these regolith weathering processes, instead reflecting deeper weathering reactions (>9.3 m). Our work thus shows that the δ⁷Li of waters draining highly weathered catchments may reflect bedrock mineralogy and hydrology, rather than weathering intensity in the regolith covering the catchment.