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Identifying priority conservation areas is essential for minimizing the loss of biodiversity. Aquatic plants are of particular interest because their contribution to biodiversity is poorly understood and they play a central role in aquatic inland ecosystems. This study thus aimed to identify the areas on the Iberian Peninsula that contain the most aquatic plant species. It also explored the effectiveness of the Natura 2000 network in conserving aquatic plants. To describe macroecological patterns of aquatic plant richness, species distribution models based on bioclimatic factors were generated using maximum entropy modelling. The results were used to identify high-richness areas of potential conservation interest. Employing gap analysis, the overlap between these areas and the Natura 2000 network was examined to evaluate the effectiveness of the network. The species studied had been recorded in just 34.98% (2172/6209) of the Universal Transverse Mercator (UTM) grid cells examined, meaning that 65.02% of the cells contained no species records. The gap analysis indicated that at least 2.27% of the cells represented areas of high conservation potential. This research underscores the limited effectiveness of the Natura 2000 network in protecting aquatic plants and shows that a high proportion of the aquatic ecosystems studied are subject to severe human pressures. The results of this work provide highly relevant and valuable information on the less-studied regions of the Iberian Peninsula. Overall, the findings presented here should greatly inform the development of more objective strategies for conserving zones with a high diversity of aquatic plants. The information acquired should be used in future efforts to identify new priority conservation areas and assess those already in place.