The rise of global surface temperature by between 1.2 °C and 4 °C by 2100 is expected to affect freshwater ecosystems and the growth of aquatic plants. By extending the distribution range of invasive macrophytes, climate warming could increase their management costs. The aim of this study was to test the impact of a 3 °C warming in spring and in summer on the morphology and physiology of two native species (Mentha aquatica, Myosotis scorpioides) and two invasive species (Ludwigia hexapetala, Myriophyllum aquaticum) under controlled conditions. Our study showed that the increase of spring temperature induced morphological modifications for all species, while a 3 °C warming induced changes in carbohydrates composition for native species in spring, and modification of carbohydrate content for invasive species at both seasons. Patterns of carbohydrate content group the two invasive species together, possibly highlighting common physiological mechanisms. Moreover, the increase of spring temperature favoured the apical and/or lateral growth solely for invasive species. Hence, the invasive species specific response to warming suggests that higher temperature may favour their growth in spring, which might allow them to colonise the water column earlier than natives. This competitive advantage could affect aquatic ecosystems functioning and biodiversity in the coming years.