Wetlands are important to continental evolution, providing both the arenas and refugia for emerging and declining biotas, respectively. Based on this significance and the high preservation potential, the resulting fossiliferous deposits play a key role in understanding past and future biodiversity. We reconstruct the trophic structure and age of the early Permian Manebach-Lake ecosystem, Germany, thriving in a wetland when the tropical biosphere faced profound upheaval in the peaking Late Palaeozoic Icehouse. Nine excavations, the high-resolution, spatiotemporal documentation of fossils and sediments, and the U-Pb radioisotopic dating of tuffs allow us to distinguish autogenic and allogenic factors that shaped the limnic biocoenosis. The Manebach Lake was an exorheic, stratified, perennial water body in the 10¹–10² km² scale, integrated into the catchment draining much of the European Variscides. Lake formation paralleled an Asselian regional wet climatic interval and benefited from rising groundwater tables due to post-Variscan tectonics. Stromatolite-forming cyanobacteria, bivalves, several crustacean groups, amblypterids resembling Paramblypterus duvernoyi and xenacanthid sharks formed a differentiated biocoenosis. Digestive remains prove the rare presence of acanthodians, branchiosaurs, and large tetrapods. Anoxic events affected the mainly epilimnal community. The results indicate woody-debris-bearing lake littorals devoid of semi-aquatic and aquatic plants as places suitable for large stromatolites to grow, underpin the model of declining freshwater shark diversity in most Permian Variscan basins, demonstrate fish/amphibian ratios in limnic taphocoenoses to measure lake perenniality and reveal taphonomic biases in freshwater plant assemblages. Our outcomes highlight the need for more knowledge about the diversity, ecology, and fossilisation pathways of past limnic biotas, particularly microorganisms and actinopterygian fishes, to reconstruct deep-time continental ecosystems.