In 2015, a breach in the Fundão Dam in Mariana (Minas Gerais State, Brazil) resulted in the release of contaminated tailings into the Doce River basin. This accident increased the concentrations of arsenic (As), lead (Pb), cadmium (Cd), vanadium (V), and manganese (Mn) in the soil, posing a potential hazard to the physiology of native species. Therefore, this study aimed to assess whether chlorophyll a fluorescence (ChlF) in Allagoptera arenaria and Guapira pernambucensis changed following this accident when tested under different precipitation regimes in relation to soil properties, and heavy metal absorption. Our research was conducted in the Environmental Protection Area of Conceição da Barra (APA) and the Comboios Biological Reserve (RBC) located in the state of Espírito Santo, Brazil, south-eastern Brazil. Five independent biological replicates of A. arenaria and G. pernambucensis were selected at each site for nutritional and chlorophyll a fluorescence analysis. Soil samples from APA and RBC had similar metal concentrations and physical properties. Five years after the dam rupture, A. arenaria had absorbed As, Pb, and V. The increased amounts of heavy metals absorbed did not significantly impair the OJIP curve configuration in both species during the evaluated periods. However, A. arenaria at RBC during the rainy season showed increases in the values of φR0, φP0, PITOTAL, and φE0. Cluster analysis indicated that ChlF in both species was more sensitive to variations in heavy metals within plant tissues. Then, ChlF variation indicated that A. arenaria and G. pernambucensis exhibited an acclimation strategy in response to increased absorption of heavy metals.