The various types, textures, and compositional zoning of pyrite in the gold-bearing saddle reefs, quartz veins, and surrounding sedimentary rocks provide new information on the potential source and timing of gold and arsenic and related fluid processes responsible for mineralization at Bendigo. Nodular diagenetic pyrite in the black shale tops to sandstone turbidites is enriched in invisible gold and arsenic with mean values of 0.61 ppm Au, 1,300 ppm As, and Au/Ag <1, based on LA-ICPMS analyses. Other elements enriched in the diagenetic pyrite within the organic-rich shales are Mn, Zn, Mo, Cu, V, Ba, Ag, Cd, Tl, Co, Ni, Bi, Pb, and Te. In contrast, euhedral- and growth-zoned hydrothermal pyrite in the turbidites and bedding-parallel laminated quartz veins contains lower contents of most trace elements but has higher contents of invisible Au and As, especially on the outermost rim of the pyrite. The gold-rich pyrite rims generally become thicker (a few to hundreds of microns) in proximity to the gold-bearing saddle reefs. Pyrite in the reef commonly has the highest levels of invisible Au and As and the lowest levels of other trace elements. It is characterized by Au/Ag >1 and Au/Pb >0.01. In the deepest stratigraphic levels, below known productive gold reefs, diagenetic pyrite in the most carbonaceous shales has been replaced by pyrrhotite during metamorphism. LA-ICPMS analyses reveal that the disseminated pyrrhotite contains similar levels of Ni and Co to the diagenetic pyrite but is strongly depleted in As and Au. The spatial relationships between organic-rich shales, folded bedding-parallel laminated quartz veins, and gold-arsenic-bearing saddle reefs, combined with the consistent trends in the trace element composition of pyrite hosted by these three geological elements, is interpreted to indicate that the black shales were an initial source of Au and As, and the laminated quartz veins acted as the initial pathways for hydrothermal fluid flow carrying Au and As from the source shales to the saddle reefs. Maximum gold and arsenic input into the reefs, principally as free gold plus arsenopyrite, occurred late during deformation toward the end of the hydrothermal cycle and is expressed by the Au-As-rich rims to hydrothermal pyrite in the sedimentary host rocks, laminated quartz veins, and reefs. This corresponds with final fold lockup and the development of through-going fault arrays linking adjacent anticlines. The source of Au and As for this final, and most economically important, fluid-flow event is considered to be from carbonaceous shales deeper in the basin, where original gold-bearing diagenetic arsenian pyrite reacts with organic matter and is converted to pyrrhotite, with release of Au, As, and S to the metamorphic fluid.