The detrital clay mineral assemblage contained within sedimentary archives has long been used as a proxy for palaeo-tectonic, -climate, and -environmental reconstructions as well as provenance analysis of sediments. However, many clay minerals such as smectite are highly reactive and thus prone to post-depositional alteration, or commonly form diagenetic replacement phases, which can fundamentally change clay abundance and composition within sedimentary successions. Although a critical requirement for making robust palaeo-environmental reconstructions, there are difficulties in distinguishing and quantifying clay minerals of detrital versus diagenetic origin in fine-grained sediments and in sedimentary rocks using bulk analytical techniques. A new generation of electron imaging and mineral mapping tools, optimized for analyzing fine-grained geo-materials, has the potential to resolve this long-standing challenge, if diagnostic criteria to systematically differentiate (clay) minerals of varying origin can be established. Here we define the petrographic criteria required to differentiate various classes of detrital and diagenetic illite, chlorite and kaolinite/dickite, based on a case study of continental palaeo-weathering recorded in late Neoproterozoic sequences of the Adelaide Geosyncline, South Australia. Comparison to quantitative XRD data demonstrates the accuracy of SEM-based mineral identification and quantification. After correcting for the effects of diagenesis, the original sediments are shown to have an immature mineralogy (e.g., high abundance of feldspar: 23–33% and detrital mica/2M1 illite: 7–26%, no pedogenic clays), indicative of limited chemical weathering in the late Cryogenian Enorama Shale and the early Ediacaran Brachina Formation. The mid-Ediacaran Bunyeroo Formation, by contrast, is characterized by a substantially higher content (~20–23%) of pedogenic 1M and 1Md illite coupled with trace amounts of readily weathered phases such as feldspar (~1–4%). This is indicative of enhanced chemical weathering, consistent with previous studies arguing for a growing influence of biologically-mediated pedogenic weathering in the Ediacaran.