Isopachs of Huronian strata of the Elliot and Hough Lake groups in the southern part of the Cobalt Basin can be used to define the geometry of a 4 km wide valley system that directly influenced the location of gravel-bed rivers bearing detrital gold and auriferous pyrite in the Mississagi Formation. Distribution and thickness of these and underlying formations can be directly linked to initial valley formation parallel to existing north-south-oriented faults in the Archean basement. Thickness distributions were directly influenced by active subsidence associated with transverse, east-south-east (ESE)-oriented, normal faults, related to extension along the Huronian transform-rift margin further south. Strata underlying the Mississagi Formation were largely removed by erosion in the northern part of the paleovalley system, but thickened and then thinned south of the ESE faults. Pyrite and detrital gold in the Mississagi Formation may have been concentrated from reworking of coarse clastic rocks of the Matinenda and Ramsay Lake formations, along with significant contributions from erosion of proximal Archean basement within 3–5 km of the preserved basin margins. There is strong evidence to suggest that stream flow was initially concentrated in three main structurally influenced valley systems in the north, with one lateral tributary in the south-eastern part of the basin. The fluvial systems merged, and thickened, south of the Tee Lake fault, possibly reflecting trans-tensional influences on the basin margin faults.