In the European Water Framework Directive, zooplankton was not included as a Biological Quality Element despite its important place in the aquatic trophic web. In the present study on zooplankton abundances and biomasses, we used several metrics to test their ability to detect differences among trophic statuses and ecological potential levels, and collected a large sum of data in more than 60 reservoirs at Ebro watershed, on more than 300 sampling occasions over 10 years. Our results indicate that most zooplankton metrics are correlated to environmental variables that determine reservoirs’ trophic states, especially chlorophyll a and total phosphorus. The metrics with better sensitivity to differentiate trophic states and ecological potential levels were ZOO (total zooplankton), LZOO (large zooplankton), CLAD (cladocerans), and ZOO:CHLA (zooplankton:chlorophyll a ratio). Microcrustacean metrics such as DAPHN (Daphnia), COP (copepods), CYCLO (cyclopoids), and CALA (calanoids) were good at differentiating between high and low water quality in trophic status (oligotrophic–eutrophic) and ecological potential (good or superior–moderate). Thus, zooplankton can be used as a valuable tool to determine water quality; we believe that zooplankton should be considered a Biological Quality Element within Water Framework Directive monitoring programs for inland waters.

Coastal lagoons are recent geological formations, crucial biodiversity hot-spots, and fragile ecosystems which provide several ecosystem services. These areas are strongly affected by nutrient inputs, which can lead to eutrophication and algal blooms. We identified nine Italian coastal lagoons with a surface area greater than 10 km². Most of them were previously classified in a poor ecological condition. Therefore, we used remote sensing, in particular Sentinel-2 images, to assess the trophic state of these areas over time from 2015 until 2025. Automatic products of chlorophyll-a (Chl-a), total suspended matter (TSM), and water transparency (kd_z90max) were derived. Chl-a concentrations indicated predominantly eutrophic conditions, ranging from 0.44 (Mare Piccolo) to 80.81 mg·m⁻³ (Comacchio). Comacchio and Cabras showed persistently high Chl-a values and low transparency, while Mare Piccolo was characterized by high transparency and oligotrophic conditions. Varano and Cabras showed a significant increase in Chl-a (p < 0.05) coupled with an increase in TSM (p < 0.01) and decline in transparency in Varano (p < 0.05). Most other lagoons showed no long-term trends but remained in eutrophic–hypereutrophic states. Therefore, the Italian coastal lagoons studied are vulnerable areas to environmental degradation. Many of the lagoons showed persistent eutrophic conditions and no long-term recovery trends. However, among the lagoons, there were heterogeneous ecological conditions, ranging from oligotrophic (Mare Piccolo) to chronically hypereutrophic (Comacchio, Cabras). Water clarity was mainly affected by suspended solids; however, in some cases, there was a key role in primary production (algal blooms). Sentinel-2 data proved effective for monitoring spatial and temporal variability in coastal lagoon water quality, offering a valuable tool for environmental management and early detection of degradation trends.

In the global warming context, adaptive management strategies involve the conservation and restoration of inland waters by planning the reintroduction of macrophytes to substantially mitigate greenhouse gas emissions (GHG). The selection of appropriate species is crucial. We studied the influence of two submerged macrophyte species on GHG production, sediment-oxygen microprofiles, and microbial community composition under two thermal regimes by means of a microcosm experiment. We chose the phanerogam Myriophyllum spicatum, more typical of meso-eutrophic habitats, and the charophyte Chara hispida, more frequent in oligotrophic waters and belonging to a much less studied macrophyte group, which, moreover, exhibit contrasting functional traits (i.e., roots versus rhizoids). The presence of both macrophyte types considerably reduced the diurnal diffusive CO₂ emissions due to their photosynthetic activity compared to bare-sediment situations. The radial oxygen loss of M. spicatum roots provided aerobic-microaerobic conditions beyond the first sediment centimeter, in contrast to more anoxic sediments created by C. hispida. As a result of this, each type of macrophyte determined a particular sediment microbiome. Despite dissolved CH₄ being greater in the presence of plants, no statistical differences in CH₄ diffusive flux caused by the presence or absence of plants was found. We demonstrated how the presence, or not, of macrophytes is more important than warming (in our case with a temperature difference of 3 °C) in relation to GHG emissions. Both species, being perennial, provide ecosystem services year-round and are strong candidates for management strategies aimed at transforming new or restored aquatic ecosystems into carbon sinks.