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Macrophytes are at the base of many lake food webs providing essential food resources for animals at higher trophic level, such as invertebrates, fish and waterbirds. However, data regarding the spatiotemporal variation in isotopic composition of macrophytes are generally missing. We measured the carbon and nitrogen stable isotope ratios of Charophytes at Lake Constance, where they constitute a major food source for waterbirds. Our data reveal seasonal and site-specific differences as well as depth-specific variations in isotopic carbon values within the littoral zone. Charophytes were enriched in (13)C at sites of higher productivity: the δ(13)C values were high in summer, at shallow and at relatively nutrient-rich sites, and comparatively low in winter, and in deeper and nutrient-poorer sites. In contrast, no temporal or spatial trend was found to explain the variability in the isotopic nitrogen values. These results imply that the seasonal timing of food intake (relative to turnover rates of consumers tissue) and the potential depth of foraging need to be taken into account when calculating the relative contribution of energy sources to diets of consumers such as waterbirds.