To further develop boron isotopes as a tool for understanding shale weathering, we explored patterns of boron concentrations and isotopes across the forested Susquehanna Shale Hills Critical Zone Observatory (CZO). We present boron measurements for all watershed components that provided a foundation for examining water-rock interactions in a shale dominated watershed, including water compartments (e.g., precipitation, stream water, groundwater) and solid compartments (e.g., soil, bedrock, stream sediments, suspended load, and leaf litter). Results show boron isotopes (δ11B) in the bedrock (− 4.6‰) and soil (− 5.9 to - 4.2‰) were very similar. All waters were enriched in 11B by comparison: precipitation (7.2 to 22.6‰), stream (10.3 to 15.5‰), and groundwater (2.2 to 17.4‰). Modeling revealed that isotopic fractionation observed in the surface water and groundwater could mainly be explained by water-rock interactions including clay mineral dissolution (e.g., chlorite) and coprecipitation/adsorption processes (e.g., coatings on illite particles), likely in the near surface soils (~2 m deep). We found that leaching, the loss of boron from vegetation to stream water, plays a secondary role. Specifically, such leaching likely contributes the equivalent of 10 to 26% of the B fluxes from the watershed outlet. Boron mass balance between bedrock and precipitation inputs and the exported flux of dissolved and solid pools identified a “missing” isotopically light solid flux (δ11B of −12.2 ± 5.3‰ at ~4.4 ± 3.8 mol/ha/y of B; uncertainty reported as 2 SD). We did not sample any pool with this isotopic signature. Here our data suggest the composition of this pool is more likely related to precipitation of secondary clays rather than adsorption or (co)precipitation on Fe oxides. We propose two hypotheses to explain the missing light B pool: 1) a significant portion of the particles carrying the missing 10B are not sampled because they enter groundwater at depth and are transported out of the catchment under the stream; and/or 2) the inputs and outputs of boron are not operating at steady state in the catchment today, suggesting that the missing boron particles were lost in the past in proportions higher than today. When this B budget is paired with studies of δ26Mg and δ56Fe from Shale Hills, both of which also show missing isotopic pools, the pattern indicates a fundamental gap in understanding of shale weathering. We concluded that light B particles, presumably generated in the upper soils, are likely transported deep beneath the surface in the groundwater system or episodically in the past through riverine fluxes. •Boron isotopes and concentrations at Shale Hills are controlled by clay mineral weathering, while biotic processesplay a secondary role•Boron mass balance revealed that this shale system is characterized by an unconstrained or “missing” pool of isotopically light boron•The boron isotopic composition is best explained by a “missing” pool of particles comprised of clay minerals or coatings on primary minerals