These drugs act on the fungal cell membrane, where they interfere with permeability and with transport functions. The primary action is its ability to form large pores in the membrane. The hydrophilic core of polyene antifungals form a transmembrane ion channel, resulting in ion balance disturbances, including the loss of intracellular K+.

Nystatin is used topically, and can be used by mouth as it is very poorly orally absorbed. It is highly toxic if given systemically. Amphotericin is given intravenously, and is also toxic. Lipid formulations of amphotericin allow larger doses to be given safely.
Different brands of amphotericin have different dosing recommendations, therefore the brand of amphotericin to be used should be specified when prescribing.
Close monitoring of intravenous treatment is needed.
Amphotericin is poorly absorbed when given orally and is hence administered by slow intravenous infusion. It is a highly protein-bound molecule and as such penetrates tissues and membranes (such as the blood-brain barrier) poorly. It is found in inflammatory exudates and may pass the blood brain barrier more readily when meninges are inflamed. It is excreted, very slowly, by the kidney. Residues may be found in the urine over 2 months post treatment.