River floodplains are composed of a shifting mosaic of aquatic and terrestrial habitats. Each habitat type exhibits distinct environmental and ecological properties. Temperature is a key property driving ecological processes and controlling the composition and distribution of biota. However, given the size and complexity of floodplains, ground surveys based on point measurements are spatially limited. In this study, we applied thermal infrared (IR) imagery to quantify surface temperature patterns at 12-15 min intervals over 24 h cycles in two near-natural Alpine river floodplains (Roseg, Tagliamento). Furthermore, vertical temperature distribution was measured at 3-5 min intervals in unsaturated gravel sediment deposits (at 1 cm distances; 0-29 cm depth). Each habitat type exhibited a distinct thermal signature creating a complex thermal mosaic. The diel temperature pulse and maximum daily temperature were the main thermal components that differentiated habitat types. In both floodplains, exposed gravel sediments exhibited the highest diel pulse (up to 23°C), whereas in aquatic habitats the pulse was as low as 11°C (main channel in the Roseg floodplain). In the unsaturated gravel sediment deposits, the maximum diel kinetic temperature pulse ranged from 40.4°C (sediment surface) to 2.7°C (29 cm sediment depth). Vertically, the spatiotemporal variation of temperature was about as high as horizontally across the entire floodplain surface. This study emphasized that remotely sensed thermal IR imagery provides a powerful non-invasive method to quantitatively assess thermal heterogeneity of complex aquatic and terrestrial ecosystems at a resolution required to understand ecosystem processes and the distribution of biota.