This study examined trace-element concentrations in 39 sediment samples collected in the vicinity of the abandoned Coval da Mó mine, and evaluated the anthropogenic contaminant effects and other environmental variables in the taxonomic composition, structure and morphological changes of benthic diatom communities. The results show the existence of extremely high contamination in Pb, Zn and Cd (the mean values exceed the background values 376, 96 and 19 times, respectively) on the first 2.5 km in the water flow direction. Also Co, Cu, Mn and Ni are present in high concentrations. Dilution by relatively uncontaminated sediment reduces metal concentrations downstream, but Zn concentrations increase downstream Fílvida stream, as a result of several factors such as sewage and agriculture. To evaluate the biological effects caused by Pb, Cd and Zn, three sites were selected. In the stressed environment, near the mining area (C232), diatoms were extremely rare, however there was a slight recovery at site C79 located 2km downstream. Fragilaria capucina var. rumpens, Fragilaria cf. crotonensis and Achnanthidium minutissimum showed abnormal valves which may be related to high levels of metals. Six km downstream, in Fílvida stream (C85), an increase in species richness and diversity was registered while the relative percentage of valve teratologies was lower. In the absence of OM, nutrients and low pH the diatom community patterns must be attributed to the metal concentration at some sites. Considering that community diversity can be affected by abiotic and biotic variables and valve deformations are caused by a small number of variables, basically metals, and acid conditions, we consider the presence of teratologies as an indication of the presence of metals.