The rock record from the late Early Jurassic in southern Africa encompasses the history of voluminous continental flood basalt outpourings associated with the magmatic events in the Karoo–Ferrar Large Igneous Province (LIP) in southern and eastern Gondwana. This multiphase magmatism produced one of Earth’s largest continental flood basalt successions volumetrically and is assumed to have been a main driving mechanism in late Early Jurassic global environmental perturbations, including mass extinctions and changes in climate. In southern Africa, these Lower Jurassic flood basalts are interbedded with fossiliferous sedimentary rocks, which in turn host the last signs of ‘Karoo life’ in the form of fossil plants, invertebrates and vertebrates, including the trackways of hopping mammals and the ultimate Karoo dinosaurs. The sedimentology and palaeontology of the interbeds archived depositional and biotic processes in running water as well as in and around shallow, up to ∼10 m deep freshwater lakes and ponds in the late Early Jurassic. This study explains how a complex freshwater palaeo-habitat prevailed – albeit temporarily – in this extremely stressful environment, which was unlike any modern volcanic system. The evidence collectively points to seasonally wet, warm temperate climatic conditions during the early phases of Karoo volcanism. Moreover, the evidence in the rocks also suggests that the dynamic volcanic conditions resulted in shifting habitats that likely facilitated the migration of the ultimate Karoo biota towards the north and west, away from the main Karoo land of fire, just before Gondwana started to disassemble. This refinement of the environmental dynamics in southern Gondwana presented herein lays the groundwork for future high-resolution volcanological, geochronological and chemostratigraphical studies aimed at the nuanced understanding of the global environmental effect of the Karoo–Ferrar LIP.