A long‐term daily streamflow data set, covering the period from 1925 to 2013, was compiled for the Lena River basin, with an average record length of 49 years. Time series of mean annual daily flow (MADF) and extreme (maximum, Qmax, and minimum, Qmin) daily flows were subject to trend detection and change point detection analysis. Significant changes result mostly from rapid “breakpoint” homogeneity disruptions. Thirty one time series showed trends in MADF, 10, in Qmax, and 32 of the 55 records with nonzero Qmin, significant at p ≤ 0.05. Upward trends prevail in both mean annual and extreme flows, with average magnitudes of 47% (MADF), 56% (Qmax), and 68% (Qmin). Two to three stations in each subset showed downward trends (averaging −20%, −39%, and −38%, respectively). Abrupt changes are observed in the 1990s and early 2000s mostly in the headwaters of the basin, underlain by discontinuous permafrost.