An interdisciplinary study has been carried out on Naxos Island, located in the southern Aegean Sea (Greece), which shows Miocene geodynamic and environmental changes in a classic example of a collapsing orogen. Early to mid-Miocene siliciclastic deposits on Naxos have been shed from an uplifting mountainous realm in the south, which included a patchwork of at least four source terrains of different thermal histories. Petrography of pebbles suggests that the source units formed part of a passive continental margin succession (external Pelagonian unit), and an ophiolite succession mainly of deep-water cherts and limestones deposited on basalt substratum (Pindos unit). The continental margin source contributed rounded zircon crystals of Late Jurassic to Early Cretaceous age and broadly scattering Paleozoic zircon fission-track cooling ages. A distal pebble assemblage of Paleogene shallow-water carbonates passing into flysch-like, mixed calcarenitic and siliciclastic components with volcanic arc components is subordinately present. High-grade metamorphic components from the nearby metamorphic core complex are not present.The depositional evolution reflects increasing relief and, in some parts, a fluvial succession with rhythmic channel deposition, possibly due to runoff variability forced by orbital cyclicity. Upsection, the depositional trend indicates increasing seasonality and decreasing humidity in the source region.The Miocene sedimentary succession has been deposited on an ophiolite nappe. Juxtaposition of this ophiolite nappe occurred as an extensional allochthon during large-scale extension in the Aegean region at the margins of an exhuming metamorphic core complex.