Analysis of permafrost dynamics with a three-phase, two-component flow system coupled to heat transport is used to evaluate transient changes in groundwater seepage. Both seasonal and annual analysis of flow is conducted, assuming three warming temperature trends over a ten year period, representing three climate change scenarios. Previous results have indicated that a reduction in temporal variability of groundwater flow is expected to occur for a moderate temperature trend over long warming time periods. Here, new results indicate this is also expected for larger rates-of-change of temperature increase and over shorter time periods. Additionally it is shown that short-term annual flow variability may serve as early indicators for permafrost degradation also for greater warming trends, rather than solely relying on long-term changes in mean flows.