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Large Arctic river basins experience substantial variability in climatic, landscape, and permafrost conditions. However, the processes behind the observed changes at the scale of these basins are relatively poorly understood. While most studies have been focused on the "Big 6" Arctic rivers - the Ob', Yenisey, Lena, Mackenzie, Yukon, and Kolyma - few or no assessments exist for small and medium-sized river basins, such as the Yana and Indigirka River basins. Here, we provide a detailed analysis of streamflow data from 22 hydrological gauges in the Yana and Indigirka River basins with a period of observation ranging from 35 to 79 years up to 2015. These river basins are fully located in the zone of continuous permafrost. Our analysis reveals statistically significant (p < 0.05) positive trends in the monthly streamflow time series during the autumn-winter period for most of the gauges. The streamflow increases in a stepwise pattern (post-1981) for 17 out of 22 gauges in September (average trend value for the period of record is 58% or 9.8 mm) and 15 out of 22 gauges in October (61% or 2.0 mm). The positive trends are seen in 9 out of 19 rivers that do not freeze in November (54 %, 0.4 mm) and 6 out of 17 rivers that do not freeze in December (95 %, 0.15 mm). Precipitation is shown to decrease in late winter by up to 15 mm over the observational period. Additionally, about 10 mm of precipitation that used to fall as snow at the beginning of winter now falls as rain. Despite the decrease in winter precipitation, no decrease in streamflow has been observed during the spring freshet in May and June in the last 50 years (from 1966); moreover, five gauges show an increase of 86% or 12.2 mm in spring floods via an abrupt change in 1987-1993. The changes in spring freshet start date are identified for 10 gauges; the earlier onset in May varies from 4 to 10 d over the observational period. We conclude that warmer temperatures due to climate change are impacting the hydrological regime of these rivers via changes in precipitation type (rain replacing snow). Other factors, such as the melting of permafrost, glaciers, and aufeis or changes in groundwater conditions, are likely to contribute as well; however, no direct observations of these changes are available. The changes in streamflow can have a significant impact on the ecology of the zone of continuous permafrost, while the increasing freshwater fluxes to the Arctic Ocean can impact the Arctic thermohaline circulation.