The increasing intensity, frequency, and duration of extreme climatic events (ECEs) due to climate change pose additional pressures on seagrass habitats in lagoon ecosystems. Among these ECEs, this study investigates the impact of marine heatwaves (MHWs) on three seagrass species from Mediterranean lagoons: Cymodocea nodosa, Nanozostera noltei, and Ruppia cirrhosa. Using a near-natural mesocosm, we simulated a 20-day MHW at three intensities (+ 2 °C, + 4 °C, + 6 °C above control) during spring and summer, and assessed changes in growth, respiration, and gross primary production. Species and seasonal responses varied. C. nodosa exhibited enhanced net foliar growth in spring and stable growth in summer. N. noltei benefited from moderate warming in spring but was vulnerable to high-intensity heatwaves in summer. R. cirrhosa was resilient in spring and exhibited increased growth in summer, particularly at + 4 °C. Overall, all three species tolerated a single 20-day MHW, with relative adaptation ranked as N. noltei \textless R. cirrhosa \textless C. nodosa. A common response across species was the initiation and growth of new leaves, although less pronounced in R. cirrhosa. Our experimental approach reveals clear species- and season-specific responses to MHWs, highlighting the complexity of seagrass resilience in lagoon ecosystems. In particular, seagrasses from lagoon environments display robust short-term tolerance to MHWs, with only N. noltei showing vulnerability to the highest summer intensity. These results indicate that while lagoon species are adapted to variable environments, their resilience may be challenged by increasingly frequent and prolonged MHWs expected under future climate change.