Chytridiomycosis, a lethal fungal skin disease of amphibians, fatally disrupts ionic and osmotic homeostasis. Infected amphibians increase their skin shedding rate (sloughing) to slow pathogen growth, but the sloughing process also increases skin permeability. Healthy amphibians increase active ion uptake during sloughing by increasing ion transporter abundance to offset the increased skin permeability. How chytridiomycosis affects the skin function during and between sloughing events remains unknown. Here we show that non-sloughing frogs with chytridiomycosis have impaired cutaneous sodium uptake, in part because they have fewer sodium transporters in their skin. Interestingly, sloughing was associated with a transient increase in sodium transporter activity and abundance, suggesting that the newly exposed skin layer is initially fully functional until the recolonization of the skin by the fungus again impedes cutaneous function. However, the temporary restoration of skin function during sloughing does not restore ionic homeostasis, and the underlying loss of ion uptake capacity is ultimately detrimental for amphibians with chytridiomycosis.