The objective of the paper was to determine the influence of iron(III) ions on the growth and metabolism of fungi commonly occurring in waters: the yeast Rhodotorula mucilaginosa and filamentous fungus Cladosporium herbarum. Cells of R. mucilaginosa were shown to absorb the most iron(III) ions at a concentration of 1 mg/L iron(III) ions. Yeast cells showed a considerable increase in the content of proteins and monosaccharides, as well as biomass growth. At higher concentrations of iron(III) ions, the yeast limited the intake of iron(III) ions, and a decrease in the basic metabolites in cells was observed, as well as an increase in the secretion of such metabolites into the medium. Moreover, the activity of antioxidant enzymes increased in the fungal cells, suggesting that iron(III) ions have a toxic effect. Simultaneously, even at high concentrations of iron(III) ions in the medium, no decrease in the yeast biomass was recorded. It seems therefore that the potentially pathogenic R. mucilaginosa will likely be present in waters moderately contaminated with iron(III) ions. It can be useful as a water quality bioindicator. A considerably higher capacity for the biosorption of iron(III) ions was recorded for the filamentous fungus C. herbarum. Defensive mechanisms were observed for C. herbarum, which were manifested in a substantial increase in the content of proteins and monosaccharides, as well as an increase in the activity of antioxidant enzymes, particularly under the influence of high concentrations of iron(III) ions. Moreover, it was evidenced that in the filamentous fungus, iron(III) ions limited the extracellular secretion of metabolites. These results suggest that the fungus can actively accumulate iron(III) ions and therefore eliminate them from the aquatic environment. It can be useful in water treatment processes, which has a significant impact on water ecology.