We compared morphometric and physico-chemical characteristics of farm ponds and natural wetlands in Andalusia (southern Spain) to determine whether artificial waterbodies might act as alternative and/or complementary habitats for aquatic biodiversity. Farm ponds were much smaller than natural wetlands, making them unsuitable for species requiring large waterbodies. However, we observed high farm pond density in areas lacking natural wetlands, which suggests a prime role for the conservation of species with low dispersal capacities. Natural-substrate ponds were abundant in traditional extensive farming systems and showed shoreline complexity as high as the most complex natural wetlands. Areas with more intensive agriculture were dominated by artificial-substrate ponds and wetlands, with low physical complexity in both. The high copper load in sediments, due to the use of copper sulphate as biocide, differentiated the artificial-substrate ponds from natural-looking ponds and all natural wetland types. Aqueous mineral levels in farm ponds were much lower than in natural wetlands. We can conclude that farm ponds might play a principal role in region-wide habitat complementarity, by providing a relatively high density of small, permanent, oligohaline waterbodies that is not matched by natural wetland. To enhance this role, measures regulating both pond construction and management are needed, particularly for artificial-substrate ponds.