River runoff from the four largest Siberian river basins (the Ob, Yenisei, Lena, and Kolyma) considerably contributes to freshwater flux into the Arctic Ocean from the Eurasian continent. However, the effects of variation in snow cover fraction on the ecohydrological variations in these basins are not well understood. In this study, we analysed the spatiotemporal variability of the maximum snow cover fraction (SCFmax) in the four Siberian river basins. We compared the SCFmax from 2000 to 2016 with data in terms of monthly temperature and precipitation, night‐time surface temperatures, the terrestrial water storage anomaly (TWSA), the normalised difference vegetation index (NDVI), and river runoff. Our results exhibit a decreasing trend in the April SCFmax values since 2000, largely in response to warming air temperatures in April. We identified snowmelt water as the dominant control on the observed increase in the runoff contribution in May across all four Siberian river basins. In addition, we detected that the interannual river runoff was predominantly controlled by interannual variations in the TWSA. The NDVI in June was strongly controlled by the timing of the snowmelt along with the surface air temperature and TWSA in June. The rate of increase in the freshwater flux from the four Siberian rivers decreased from 2000 to 2016, exhibiting large interannual variations corresponding to interannual variations in the TWSA. However, we identified a clear increase trend in the freshwater flux of ~4 km3/year when analysing the long‐term 39‐year historical record (1978–2016). Our results suggest that continued global warming will accelerate the transition towards the earlier timing of snowmelt and spring freshwater flux into the Arctic Ocean. Our findings also highlight the effects of earlier snowmelt on ecohydrological changes in the Northern Hemisphere.