The use of stable isotopes to identify the structure of aquatic food webs is predicted upon there being significant and consistent differences in the isotopic composition of the various classes of primary producers. The structure of food webs will be interpreted incorrectly if variations in the isotopic composition of primary producers are not taken into account. We detected significant temporal and spatial variations in the δ13C and δ15N values of aquatic plants collected from three small, lentic water bodies in south-eastern Australia. Carbon- and nitrogen- isotope values of individual taxa could each vary by up to 10 delta units, according to site and season. The magnitude of these variations is sufficiently great for them to have important consequences for the interpretation of aquatic food webs. Greater attention must be given to fluctuations in the isotopic signatures of the primary producers if the structure of aquatic food webs is to be properly understood.