Historically, the role of the Galapagos Islands has been considered critical due to the evolutionary diversification induced by natural and historical isolation. The Galapagos National Park was established in 1959, based on its historical importance associated with Charles Darwin's voyage and its rare and endemic biodiversity, composed of unique vertebrate and plant communities (Rozzi et al. 2010). In 1978, the Galapagos Islands were declared a UNESCO World Heritage Site, a critical factor associated with this national park (Rozzi et al. 2010). The Galapagos Islands are a pristine area with local and regional climates influenced by the interaction of ocean currents and winds driven by the Inter-Tropical Convergence Zone; ITCZ (Conroy et al. 2008, Trueman and d'Ozouville 2010). The long-term programme includes forty natural aquatic ecosystems (lakes, ponds, lagoons and swamps) that will be sampled on the islands of San Cristobal, Santa Cruz, Isabela and Floreana, where possible along a lowland-highland gradient. The number of sampling points will vary according to environmental heterogeneity and the presence of a littoral region, among other factors.