Location and date associated with carbon and nitrogen stable isotope ratios of European flounder larvae and potential sources of organic matter supporting their diet, as well as outputs of the stable isotope mixing model to quantify the diet contributions from the various sources of organic matter. This dataset is associated with the following publication: Dias, E., A.G. Barros, J. Hoffman, C. Antunes, and P. Morais. Habitat use and food sources of European flounder larvae across an estuarine gradient. Regional Studies in Marine Science. Elsevier B.V., Amsterdam, NETHERLANDS, 34: 101196, (2020).