The water temperature characteristics of the Lena River at basin outlet during the summer season (June–September) are considered. The analysis is based on long-term data series covering the period from the beginning of observation (1936) to the present time at Kusur (Kyusyur) station and complementary data at several stations downstream and one station upstream. These additional 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 200 km downstream to the north at Habarova (Khabarova) station have almost always been an anomalously large and negative for the considered period since the beginning of observation during open water season from July to September. The description of this difference and its analysis are presented. To sort the problem out, we consider the observational data in terms of the hydrology and morphology of the Lena River delta and main channel area, apply statistical and deterministic modelling approaches.