The Lagunas de Campillos Natural Reserve and adjacent ponds are fundamentally surrounded by regularly fertilized crop fields and livestock industry, producing leachates which can be found in the ponds. The interest in this Site of European Importance and the RAMSAR wetland complex lies in the habitats within it, which are included in the Directive on Habitats of Community Interest. It is essential to determine the trophic status of the ponds and the quality of these habitats, as well as whether corrective measures need to be established in order to maintain a good environmental status. To characterize and compare the ponds, different parameters were measured, such as conductivity, pH, nutrient concentration, Chl-a concentration, phytoplankton composition, phytoplankton abundance (<20 µm), and the quantification of heterotrophic microorganisms indicating contamination of the aquifers. The obtained results showed that all ponds, except a mesotrophic pond, are eutrophic or even hypertrophic, with high levels of total nitrogen (>8 mg L−1), total phosphorous (>165 μg L−1), and chlorophyll-a concentration. These findings explain the high densities of phytoplankton observed, with the predominant presence of small cells (<3.6 μm ESD). In addition, concentrations of heterotrophs and coliforms are, in some ponds, higher than expected. Eutrophication hinders ecological functions and ecosystem services, which finally affects biodiversity and human wellbeing. Five of the six analyzed ponds are within various protection figures for their essential importance to local and migrating avifauna. Therefore, ponds’ status analysis and the implementation of measures for maintaining ecosystem services and trophic state are fundamental for the sustainable management of the studied area.
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