Study regionThe proposed methodology has been applied in the Segura River basin (south-eastern Spain) whose hydrological regime has a high anthropic alteration and catastrophic floods have occurred at different times for centuries. The climate is generally semi-arid, with frequent droughts but also floods caused mainly by rainfall associated with mesoscale convective systems. Study focusWe present a methodology that exploits all available information to obtain reliable low-frequency flood quantiles through the integration of different methods. First, a Weather Generator (WG) was implemented with the results from a regional study of annual maximum precipitation. Second, a rainfall temporal disaggregation procedure was carried out to capture the sub-daily behavior of flood generating storms. Third, a fully-distributed Hydrological Model (HM) was implemented including the role of sediments in extreme events. Finally, the estimation of flood quantiles using plotting positions was validated with systematic and non-systematic information. New Hydrological Insights for the regionThe use of this process-based approach allows to reproduce the main hydrometeorological mechanisms associated with floods in the region studied. Accurate flood quantiles up to 200 years have been possible to obtain, which represents an important advance in the knowledge of the basin since reliable flood quantiles of only 20 years were adequately captured with the current observations. Finally, sediment yield has been proven to be an important factor for the region hydrographs’ reconstruction.