Water temperature is known to influence individual animal metabolism, development, and reproduction. However, in situ studies aiming to demonstrate the link between water temperature and community structure in complex ecosystems such as large river floodplains are still rare. In particular, we have little indication about how an increase in temperature affects the density of native and invasive species within a community. Large river floodplains cover a varied range of environmental conditions, are rich in species, and therefore potentially useful ecosystems to study the effect of water temperature at the community level. Moreover, as freshwater communities are increasingly impacted by global warming and biological invasions, an improved understanding of the possible interaction between these drivers would be beneficial. First, we studied during two years the thermal heterogeneity of 36 sites in a large river (Rhone) floodplain. Second, we compared the thermal regimes of sites having different levels of hydrological connectivity with the main river channel. Third, we studied the combined and separated effects of the thermal regime and the hydrological connectivity on the presence and densities of native and non-native species of macroinvertebrates. The studied large river floodplain covered a wide range of thermal regimes, with some sites displaying a yearlong constant temperature of about 10°C, whereas others experienced thermal amplitude of over 25°C. The thermal regime was independent of the level of hydrological connectivity of the sites. The increase in hydrological connectivity had a significant and positive effect on the richness of non-native species within sites. The thermal regime had a positive influence on the density of non-native species but no effect on the total density of native taxa within communities. This study showed that large river floodplains possess a wide range of thermal conditions and that the increase in water temperature can have a positive influence on the presence of non-native populations of macroinvertebrates. This study provides a first set of empirical results to establish models predicting the effect of increasing temperatures on the establishment of non-native and native species in a complex ecosystem and underline the problem of biological invasions under climate change.