The water temperature characteristics of the Lena River at basin outlet during the summer season (June to September) are investigated. The analysis is based on a long-term data series covering the period from the beginning of observations (1936) to the present time (2012) at Kusur (Kyusyur) gauging station and complementary data at several stations downstream and one station upstream. These complementary data are rarely used, but their analysis is important for understanding processes in the basin outlet area. The differences between the stream surface temperatures at Kusur station and Habarova (Yu. A. Khabarova) station 200 km downstream to the north have almost always been anomalously large and negative during open water season from July to September since the beginning of observations. The description of this difference and the analysis of its possible causes are major focuses of the article. To sort the problem out, we consider the large observational database in terms of the hydrology and morphology of the Lena River delta and main channel area collected from different sources and apply statistical and deterministic modelling approaches. The inability of water temperature measurements, which were taken near the right river bank, to represent the mean cross-sectional temperature at Kusur station is addressed. We also analyze the water temperature trends at both Kusur and Habarova stations.