Species population trajectories mostly arise from the combined influence of anthropogenic disturbance, biotic interactions and abiotic factors. However, assessing the relative contribution of these drivers remains challenging, as long-term ecological datasets, essential for robust inference, are scarce. We examined the population dynamics of the co-occurring sea urchins Paracentrotus lividus and Arbacia lixula using time series spanning up to 33 years from two Western Mediterranean Marine Protected Areas (MPAs): Medes (Spain) and Tavolara Punta Coda Cavallo (Italy). We quantified long-term population trends, assessed the influence of climatic, hydrodynamic and trophic drivers, and identified abrupt shifts in population trajectories. Generalised additive (mixed) models were combined with structural breakpoint analyses i) to investigate both contemporaneous and lagged effects of marine heatwaves (MHWs), storm-driven wave exposure and predatory fish biomass, and ii) to identify abrupt shifts in population trajectories. Our time series analysis showed that while P. lividus has declined consistently across the two MPAs, regardless of protection status, A. lixula has remained fairly stable at Medes and underwent only a moderate decline at Tavolara Punta Coda Cavallo. Lagged cumulative MHWs intensity, emerged as the strongest predictor of P. lividus population decline. Storm-driven wave impact provided an additional source of mortality at highly exposed sites. Breakpoint analyses identified abrupt and persistent reductions in P. lividus density at Medes, followed by limited evidence of population recovery. By contrast, A. lixula exhibited weak and inconsistent responses to MHWs and no detectable response to storm impact, likely reflecting its greater thermal tolerance and morphological adaptations to hydrodynamic stress. These different trajectories are progressively altering rocky-reef sea urchin assemblage composition. Our results highlight the role of extreme climatic events as key drivers of Mediterranean sea urchin dynamics, with potential consequences for herbivory, trophic regulation, rocky-reef community structure and ecosystem functioning as extreme events become increasingly frequent.