The objective of this study is to evaluate the effects of physical-chemical and biological variables of the water of the Capibaribe River (state of Pernambuco, Brazil) on leaf anatomy, including ultrastructure and photosynthetic pigment of Salvinia auriculata. Specimens of S. auriculata collected in the Gurjaú River, an area with a low pollution degree, were acclimatized in Hoagland's solution and then subjected to three water samples of the Capibaribe River with different levels of pollution. Twenty-one physical-chemical and biological variables were analyzed according to the Standard Methods for the Examination of Water and Wastewater. The results showed that the samples of the Capibaribe River presented nine parameters that did not comply with the current Brazilian legislation. After 15 days of bioassay, S. auriculata presented variations in mesophyll and cuticle thickness, changes in trichome morphology and accumulation of phenolic compounds. No significant differences were observed for photosynthetic pigment content and leaf length of S. auriculata. Multivariate analyses (PCA and Cluster) showed that the point in the Capibaribe River with the highest number of variables that do not comply with the current legislation was responsible for major structural and chemical changes observed in S. auriculata.