The Lena River (Lena R.) heat flux affects the Laptev Sea hydrology. Published long-term estimates range from 14.0 to 15.7 EJ·a−1, based on data from Kyusyur, at the river outlet. A novel daily stream temperature (Tw) dataset was used to evaluate contemporary Lena R. heat flux, which is 16.4 ± 2.7 EJ·a−1 (2002–2011), confirming upward trends in both Tw and water runoff. Our field data from Kyusyur, however, reveal a significant negative bias, −0.8 °C in our observations, in observed Tw values from Kyusyur compared to the cross-section average Tw. Minor Lena R. tributaries discharge colder water during July–September, forming a cold jet affecting Kyusyur Tw data. Major Tw negative peaks mostly coincide with flood peaks on the Yeremeyka River, one of these tributaries. This negative bias was accounted for in our reassessment. Revised contemporary Lena R. heat flux is 17.6 ± 2.8 EJ·a−1 (2002–2011) and is constrained from above at 26.9 EJ·a−1 using data from Zhigansk, approximately 500 km upstream Kyusyur. Heat flux is controlled by stream temperature in June, during the freshet period, while from late July to mid-September, water runoff is a dominant factor.