Protected area networks represent one of the mainstays of global conservation polices and are therefore central to current efforts to maintain biodiversity. However, a major limitation of most conservation strategies is their bias towards particular taxonomic groups and ecosystems, meaning that many taxa and habitats are often only incidentally protected as a by-product of inclusion within reserves. Here we investigate how effectively protected area networks, not specifically designated for freshwaters, support aquatic biodiversity in the Iberian Peninsula (Spain and Portugal), using data for water beetles, surrogates of overall macroinvertebrate diversity in these habitats. We explore the behaviour of different measures (α, β and γ) of both taxonomic and functional diversity at different spatial scales. Overall our findings highlight the contrasting performance of reserve systems in the maintenance of either taxonomic or functional diversity, as well as the importance of spatial scale. Iberian reserves perform relatively well in supporting taxonomic diversity of water beetles at the peninsular scale, but the same protected areas poorly represent functional diversity. Such a mismatch cautions against the use of any one diversity component as a surrogate for others, and emphasizes the importance of adopting an integrative approach to biodiversity conservation in aquatic ecosystems. Furthermore, our results often show contrasting patterns at smaller spatial scales, highlighting the need to consider the influence of scale when evaluating the effectiveness of protected area networks.