Climate change scenarios for sub-humid and semi-arid regions predict that current cycles of drought and flood will intensify. In shallow lakes, that means big variations on salinity due to expansion and contraction of water volume. To assess the consequences of these changes of salinity on the ecosystem, we conducted a 2-months mesocosm experiment simulating the variations of salinity found in natural small shallow lakes of the agricultural Pampean landscape, in a two treatments and a control design. In Drought Salinity Conditions (DSC) treatment, we progressively increase water salinity, while in Flood Salinity Conditions (FSC) treatment we progressively decrease water salinity. We predict that under increasing levels of salinity, functional diversity will decrease affecting all the biotic community. Submersed macrophytes and phytoplankton reached a higher biomass in FSC units, while periphyton and metaphyton prevailed in DSC treatment. Zooplankton and macroinvertebrate were also affected, being in general less abundant and diverse in the salty environment. Also fishes had higher mortality there. High levels of salinity acts as an environmental filter of biological communities and doing so shapes the arrangement of trophic interactions. The consequences of climate change hit on all the components of shallow lake ecosystems and alter their structure and function.