Anomalous fractionation of the minor isotopes of sulfur (Δ³³S, Δ³⁶S) in Archean pyrite is thought to reflect photochemical reactions in an anoxic atmosphere, with most samples falling along a reference array with Δ³⁶S/Δ³³S ≈ −1. Small deviations from this array record microbial sulfate reduction or changes in atmospheric source reactions. Here, we argue that reworking of atmospheric sulfur with distinct minor sulfur isotope ratios (Δ³⁶S/Δ³³S ≠ −1) produced additional variability in sulfide Δ³³S and Δ³⁶S-values in a 3.52 Ga hydrothermal barite deposit at Londozi, Barberton Greenstone Belt, Swaziland. In situ measurement of the four stable sulfur isotopes in pyrite revealed Δ³⁶S–Δ³³S relationships and a Δ³⁶S/Δ³³S trend (−3.2 ± 0.4), which is significantly different from the co-variation between Δ³⁶S and Δ³³S in the co-existing barite that reflects ambient Paleoarchean seawater sulfate. This argues against biological or thermochemical sulfate reduction at the time of barite deposition, and requires incorporation of sulfide generated in a chemically distinct atmosphere before 3.52 Ga. We propose a model that combines reworking of this sulfur by hydrothermal leaching, deep mixing with juvenile sulfur and surface mixing with biogenic sulfide to explain the observed variation in δ³⁴S, Δ³³S and Δ³⁶S. These interactions between abiotic and biological processes in the Londozi hydrothermal system complicate the interpretation of biosignatures based on deviations in Δ³³S and Δ³⁶S from the Archean reference array.