<p>Shallow lakes have been increasingly affected by multiple stress factors over the past decades. However, understanding these impacts on planktonic communities requires in-depth knowledge about community structure. Using a combination of eDNA-based data and a trait-based approach, the present study aims to reveal how functional diversity and resource use efficiency of phytoplankton respond to stress gradients in Central European saline ponds. Our results showed that conductivity (a proxy for salinity) and algal-free total suspended solids (a proxy for turbidity) were key environmental variables affecting functional group composition. However, the two factors influenced different aspects of trait-based diversity. While functional dispersion based on presence-absence data was positively associated with salinity and total nitrogen, presence-based functional evenness was positively correlated with turbidity. Resource use efficiency showed a positive relationship with turbidity and a negative association with salinity. These differential impacts on phytoplankton resulted in a hump-shaped diversity-resource use efficiency relationship, indicating complex interactions among dominant environmental variables, niche partitioning and community functioning. Our findings imply that interpreting the link between community diversity and performance from field observations is not straightforward without careful consideration of local environmental factors and cannot be fully explained by classical biodiversity-ecosystem functioning theory.</p>