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The widespread salinisation of freshwater ecosystems poses a major threat to the biodiversity, functioning, and services that they provide. Human activities promote freshwater salinisation through multiple drivers (e.g., agriculture, resource extraction, urbanisation) that are amplified by climate change. Due to its complexity, we are still far from fully understanding the ecological and evolutionary consequences of freshwater salinisation. Here, we assess current research gaps and present a research agenda to guide future studies. We identified different gaps in taxonomic groups, levels of biological organisation, and geographic regions. We suggest focusing on global- and landscape-scale processes, functional approaches, genetic and molecular levels, and ecoevolutionary dynamics as key future avenues to predict the consequences of freshwater salinisation for ecosystems and human societies. This work is part of the AQUACOSM and AQUACOSM-plus projects that have received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement Nos 731065 and 871081. D.C.M., M.B., E.J., R.P., S.A.B., M.G., Z.H., S.L., J.C.N., M.R., and C.F.V. were supported by the H2020 EU-funded project AQUACOSM-plus (no. 871081). D.C.M., M.B., S.A.B., and J.C.N. were supported by the H2020 EU-funded project AQUACOSM (no. 731065). M.B. and E.J. were supported by the TÜBITAK program BIDEB2232 (project 118C250). M.B. and S.B. were supported by the H2020 EU-funded project PONDERFUL (no. 869296). Z.H. and C.F.V. were supported by the NKFIH-471-3/2021 project. Z.H. was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences. P.U-C. was supported by the Swedish Research Council Formas (grant: 2020-01825). M.M. was supported by the Grant RyC2016-19348 funded by MCIN/AEI/10.13039/501100011033 and by ESF ‘Investing in your future’

International audience; no abstract

Mediterranean salt marshes are ecosystems that are highly influenced by sea changes and freshwater inputs from runoff. In these ecosystems, toxic and non-toxic algae blooms often produce large and unpredictable biomasses of phytoplankton. The Microtox R test has been described as a successful, quick method for detecting toxicity in various phytoplankton taxa. Ourstudy sought to test the efficiency of Microtox R in detecting toxic HAB in Mediterranean salt marshes. The results showed that the Microtox R test was able to detect toxic substances in the particulate matter of several lagoons in the Empordà salt marshes. This Microtox R toxicity coincided with periods when potentially harmful cyanobacteria, dinoflagellates and haptophytes had a high biomass. The results suggest that potentially harmful phytoplankton cannot be ruled out as a source of Microtox R