Small shallow lakes (SSLs) have great conservation value and support numerous ecosystem services. However, these small ecosystems are faced with many threats, including eutrophication, which tends to shift biodiverse SSLs to a turbid state dominated by phytoplankton. The ecological quality of SSLs still remains poorly evaluated because of the lack of adapted tools. We propose a new trophic index-TIM2S-based on the tolerance range of 245 macrophyte species to total phosphorus. As a single trophic index can favour oligotrophic ecosystems and their associated species to the detriment of more eutrophic but rare species, we converted TIM2S into a predictive reference-based model. Then, we compared TIM2S with five existing trophic indices in their efficiency to discriminate trophic levels and disentangle eight anthropogenic or internal pressures. TIM2S was the only index strongly correlated with total phosphorus and able to discriminate trophic levels. Most existing trophic indices are expert-based, and reflect community alteration rather than eutrophication. These expert-based indices are also dependent on numerous environmental factors, highlighting the need for robust predictive models to evaluate ecological statuses accurately. TIM2S is Water Framework Directive-compatible and can be used widely in Europe to evaluate the trophic status and trophic alterations of SSLs.