<p>This study evaluated the ecological thresholds in the phytoplankton functional structure in tropical freshwater ecosystems (river and deep and shallow lakes). We expected to find that metal contamination promotes more abrupt changes in phytoplankton functional structure, especially in shallow ecosystems. This is due to reduced water volume, frequent resuspension, and limited dilution capacity and stratification. We also expected that natural variables such as turbidity (light availability), nutrient enrichment, and grazing pressure would affect the functional structure, but with less intensity and more gradual patterns of change. Six functional traits (volume, surface/volume ratio, silica demand, heterocyst formation, mixotrophy capability, and life form) were used to define FE, and TITAN analysis identified abrupt changes along environmental gradients. Only shallow lakes exhibited more negative than positive effects, showing more sensitive FE. In the Doce River, there was a balance between sensitive and tolerant FE, while deep lakes displayed greater tolerance to increasing gradients. We found that shallow lakes are particularly vulnerable to anthropogenic effects and mining waste, while deep lakes are comparatively less susceptible to the loss of functional richness. We conclude that responses of phytoplankton functional structure to environmental stressors are not uniformly negative and vary according to ecosystem type and seasonal influences.</p>