Anastomosing rivers exhibit large spatial diversity in morphology and hydrological processes, that manifests in temporal thermal heterogeneity. This, in turn, determines the rate of biochemical processes and the distribution of aquatic macrophytes within the river ecosystem. In this study, we investigated the spatio-temporal variability of water temperature in conjunction with water level fluctuations and river discharge in an anastomosing section of the river channel. For this purpose, high resolution time series coming from eight monitoring stations located along the course of the Narew river (Poland) have been used. The spectral analyses of time series have been applied in order to identify characteristic scales and frequencies of the thermal inputs. The results revealed high spatial heterogeneity in thermal conditions associated with site-specific interactions. Moreover, spectral analyses of water temperature fluctuations show some characteristic scaling behaviour. The results obtained in this study highlight the importance of water monitoring networks for understanding complex interactions within wetland ecosystems.