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Amino acids (AAs) are critical biochemical compounds for living organisms. Because of the limited capacity for their de novo synthesis in many animals, the nutritional value of food largely depends on its AA composition relative to the animal's requirements. To improve present knowledge on AA variability in freshwater crustaceans, we studied the inter- and intraspecific variability in three contrasting species from an oligotrophic alpine lake (Daphnia pulicaria, cladocera; Cyclops abyssorum, cyclopoid copepod and Diaptomus cyaneus, calanoid copepod). Inter-species differences were larger than intraspecific variation, confirming a non-strict homeostasis in freshwater crustacean zooplankton. The intraspecific variability differed for each species: in Daphnia, it was mainly related with ontogenetic changes rather than reproduction; in Cyclops, both factors were equally important; and reproduction was the most relevant in Diaptomus. Reproduction changes were associated with serine and phenylalanine in the three species, while the AAs responsible for ontogenetic changes differed in each species. There were no gender differences in AA composition in any of the two copepod species. Free AAs formed a very low percentage of total AA pool (<2.7%). Taking advantage of the fact that Daphnia is the main prey for Cyclops in the lake studied, we further investigated to what extent the AA composition is related with Cyclops–Daphnia nitrogen stable isotope fractionation. Only those AAs that are both essential and are not trans-aminated during protein synthesis had a significant correlation with nitrogen stable isotope fractionation, supporting the hypothesis that an AA imbalance can be responsible for a variable nitrogen stable isotope fractionation. [ABSTRACT FROM PUBLISHER]