Our understanding is limited to how transient changes in glacier response to climate warming will influence the catchment hydrology in the Arctic and Sub-Arctic. This understanding is particularly incomplete for flooding extremes because understanding the frequency of such unusual events requires long records of observation not often available for the Arctic and Sub-Arctic. This study presents a statistical analysis of trends in the magnitude and timing of flood extremes and the mean summer discharge in two sub-arctic catchments, Tarfala and Abisko, in northern Sweden. The catchments have different glacier covers (30% and 1%, respectively). Statistically significant trends (at the 5% level) were identified for both catchments on an annual and on a seasonal scale (3-months averages) using the Mann-Kendall trend test. Stationarity of flood records was tested by analyzing trends in the flood quantiles, using generalized least squares regression. Hydrologic trends were related to observed changes in the precipitation and air temperature, and were correlated with 3-months averaged climate pattern indices (e.g. North Atlantic oscillation). Both catchments showed a statistically significant increase in the annual mean air temperature over the comparison time period of 1985–2009 (Tarfala and Abisko <i>p</i><0.01), but did not show significant trends in the total precipitation (Tarfala <i>p</i> = 0.91, Abisko <i>p</i> = 0.44). Despite the similar climate evolution over the studied period in the two catchments, data showed contrasting trends in the magnitude and timing of flood peaks and the mean summer discharge. Hydrologic trends indicated an amplification of the streamflow and flood response in the highly glacierized catchment and a dampening of the response in the non-glacierized catchment. The glacierized mountain catchment showed a statistically significant increasing trend in the flood magnitudes (<i>p</i> = 0.04) that is clearly correlated to the occurrence of extreme precipitation events. It also showed a significant increase in mean summer discharge (<i>p</i> = 0.0002), which is significantly correlated to the decrease in glacier mass balance and the increase in air temperature (<i>p</i> = 0.08). Conversely, the non-glacierized catchment showed a significant decrease in the mean summer discharge (<i>p</i> = 0.01), the flood magnitudes (<i>p</i> = 0.07) and an insignificant trend towards earlier flood occurrences (<i>p</i> = 0.53). These trends are explained by a reduction of the winter snow pack due to higher temperatures in the winter and spring and an increasing soil water storage capacity or catchment storage due to progressively thawing permafrost.