The implementation of physiological indicators reflecting the response of organisms to changes in their environment is assumed to provide potential benefits for ecological studies. By analysing the physiological condition of organisms in freshwater ecological studies rather than their ultimate effects, physiological indicators can contribute to a faster assessment of effects than using traditional ecological indicators, such as the evaluation of the benthic community structure or the determination of the reproductive success of organisms. This can increase the effectiveness of environmental health assessment and experimental ecology. In this respect the thesis focuses on physiological measures characterizing the energetic condition and energy consumption (the concentration of energy storage compounds, the adenylate energy charge, the energy consumption in vivo), as well as individual growth (RNA:DNA ratio) of organisms. Although these sub-individual indicators are commonly applied in marine ecology and more recently in ecotoxicology, they have been rarely applied in freshwater ecology to date. With respect to an increased use of physiological indicators in freshwater ecological studies, the objectives of the present thesis are twofold. First, it highlights the potential of assessing the individual fitness by means of physiological indicators in freshwater ecological studies. For that reason, Chapter 2 provides the basic assumptions as well as the theoretical and methodological fundamentals necessary for the application of physiological indicators within freshwater ecology and, furthermore, points out their applicability by several case studies. As second objective, the thesis addresses selected ecophysiological aspects of native and non-native freshwater amphipods, which are considered suitable candidates for the determination of physiological indicators in ecological studies due to their function as keystone species within aquatic habitats. The studies presented in Chapters 3−5 of the thesis provide information on (i) species- and sex-specific seasonal variations within the energetic condition of natural Gammarus populations (G. fossarum, G. pulex), (ii) differences in metabolic activity and behaviour between different amphipod species (G fossarum, G. roeselii and D. villosus), as well as (iii) the direct effects of ambient ammonia on the physiology and behaviour of D. villosus. The fundamental conclusions drawn from the conducted field and laboratory studies, as well as their relevance and general implications for the application of physiological indicators in freshwater ecological research are discussed in Chapter 6.