The common sulfide mineral pyrite is abundant throughout sedimentary uranium systems at Pepegoona, Pepegoona West and Pannikan, Lake Eyre Basin, South Australia. Combined chemical, isotopic and microstructural analysis of pyrite indicates variation in fluid composition, sulfur source and precipitation conditions during a protracted mineralization event. The results show the significant role played by pyrite as a metal scavenger and monitor of fluid changes in low-temperature hydrothermal systems.In-situ micrometer-scale sulfur isotope analyses of pyrite demonstrated broad-scale isotopic heterogeneity (δ34S=-43.9 to +32.4‰VCDT), indicative of complex, multi-faceted pyrite evolution, and sulfur derived from more than a single source. Preserved textures support this assertion and indicate a genetic model involving more than one phase of pyrite formation. Authigenic pyrite underwent prolonged evolution and recrystallization, evidenced by a genetic relationship between archetypal framboidal aggregates and pyrite euhedra. Secondary hydrothermal pyrite commonly displays hyper-enrichment of several trace elements (Mn, Co, Ni, As, Se, Mo, Sb, W and Tl) in ore-bearing horizons. Hydrothermal fluids of magmatic and meteoric origins supplied metals to the system but the geochemical signature of pyrite suggests a dominantly granitic source and also the influence of mafic rock types. Irregular variation in δ34S, coupled with oscillatory trace element zonation in secondary pyrite, is interpreted in terms of continuous variations in fluid composition and cycles of diagenetic recrystallization. A late-stage oxidizing fluid may have mobilized selenium from pre-existing pyrite. Subsequent restoration of reduced conditions within the aquifer caused ongoing pyrite re-crystallization and precipitation of selenium as native selenium.These results provide the first qualitative constraints on the formation mechanisms of the uranium deposits at Beverley North. Insights into depositional conditions and sources of both sulfide and uranium mineralization and an improved understanding of pyrite geochemistry can also underpin an effective vector for uranium exploration at Beverley North and other sedimentary systems of the Lake Eyre Basin, as well as in comparable geological environments elsewhere. © 2013 Elsevier Ltd.