The organic-rich upper shale member of the upper Devonian–lower Mississippian Bakken Formation (Williston Basin, North Dakota, USA) has undergone significant diagenetic alteration, irrespective of catagenesis related to hydrocarbon generation. Alteration includes precipitation of numerous cements, replacement of both detrital and authigenic minerals, multiple episodes of fracturing, and compaction. Quartz authigenesis occurred throughout much of the member, and is represented by multiple generations of microcrystalline quartz. Chalcedonic quartz fills radiolarian microfossils and is present in the matrix. Sulfide minerals include pyrite and sphalerite. Carbonate diagenesis is volumetrically minor and includes thin dolomite overgrowths and calcite cement. At least two generations of fractures are observed. Based on the authigenic minerals and their relative timing of formation, the evolution of pore waters can be postulated. Dolomite and calcite resulted from early postdepositional aerobic oxidation of some of the abundant organic material in the formation. Following aerobic oxidation, conditions became anoxic and sulfide minerals precipitated. Transformation of the originally opaline tests of radiolaria resulted in precipitation of quartz, and quartz authigenesis is most common in more distal parts of the depositional basin where radiolaria were abundant. Because quartz authigenesis is related to the distribution of radiolaria, there is a link between diagenesis and depositional environment. Furthermore, much of the diagenesis in the upper shale member preceded hydrocarbon generation, so early postdepositional processes were responsible for occlusion of significant original porosity in the member. Thus, diagenetic mineral precipitation was at least partly responsible for the limited ability of these mudstones to provide porosity for storage of hydrocarbons.