The Arctic freshwater systems plays a key role in storing and delivering sediments, organic matter and solutes downstreams to the Arctic Ocean. Climate change has led to drastic changes in the freshwater cycle, which is reflected in increased discharge and biochemical fluxes from the six large Arctic rivers coering approximately half of the Arctic drainage basin. Scaling the results to the unmonitored portion f the pan-Arctic watershed is difficult as these smaller catchments do not extend as far south and cover differing climae, permafrost and vegetation zones. Further, permafrost degradation processes, like the in situ thawing of permafrost and the occurence of physical disturbances have effects on the freshwater quality. The overall aim of this thesis was to understand biogeochemical characteristics and lateral flixes from small Arctic coastal catchments with respect to summer rainfall and permafrost degradation. Specifically, the objectives were (1) to investigate downstream changes in biogeochemistry with regard to past and present permafrost degradation in a Low Arctic setiing, (2) to assess downstream changes in dissolved organic matter (DOM) quality in different geiographic settings (Low Arctic and High Arctic) and (3) to quantify biogeochemical fluxes from a Low Arctic catchment over several summer seasons. Information on past and present permafrost degradation at Herschel Island (Yukon, Canada) was obtained by mapping physical disturbances (active layer detachment slides ALDS and retrogressive thaw slumps RTS) from aerial photographs and satellite imagery. This revealed a decrease in the total area of disturbances by 41 % and an increase of number of disturbances by 66 % between 1952 and 2015. The geospatial information of the disturbances was then linked to stream biochemistry. Hydrological connectivity of disturbances was essential to impact solute and suspend sediment concentrations from slopes, tributaries and along the stream. Degrading ice-wedge polygons were found to substantially alter the dissolved organic carbon (DOC) concentrations in the headwaters, but could not be detected at the outflow. Although there was considerable spatial variability along the streams, a linear relationship was detected between catchment size and daily DOC and solute fluxes. Sediment fluxes on the other hand were highly variable due to short-lived sediment supply and hydrologically connected physical disturbances. Thus, the magnitude to which permafrost degradation will alter biogeochemical fluxes now and in the future is dependent on hydrological connectivity. The application of absorption measurements to characterize DOM in the Low Arctic (Herschel Island) and High Arctic (Cape Bounty, Melville Island, Nunavut, Canada)showe great potential for assessing water quality changes. DOM quality and quantity were influenced by vegetation cover and soil organic carbon. Higher soil organic carbon content and the greater abundance of plant material at the Low Arctic site introduced higher lignin concentration into the aquatic system leading to a stronger color of DOm compared to the High Arctic site. Flow pathways and the deeper flow pathways led to the export of permafrost-derived DOM that had undergone microbial processing, shallow pathways enabled the export of fresh, near surface derived DOM that was seceptible to degradation. Summer rainfall, which is anticipated to increase in the future led to the activation of shallow subsurface flow pathways, thus the export of fresh DOM prone to degradation. It was found that DOM exported from small catchments studies here was much fresher and bioavailable compared to DOm delivered by large Arctiv rivers. This underlines the importance of small catchments at the pan-Arctic scale. Riverine biogeochemical fluxes from Low Arctic watershed (Herschel Island) were further studied over three summer seasons with a focus on rainfall impacts. Discharge concentration heysteresis analyses revealed flow pathways and sourcing of constituens. During baseflow conditions, water was routed through the subsurface mobilizing solutes from the mineral soil deeper in the active layer. Rainfall events activated shallow near-surface pathways and led to the export of organic material. Comparing biogeochemical fluxes per unit area to different setting showed the substantial contribution of small watersheds in routing constituents to the nearshore zone. For example, DOC fluxes were in the same range as cumulative DOC flux estimate for the large Arctic rivers, and sediment flux exceeded the estimate from Lena and Kolyma river in one year. Short-lived sediment supply from disturbances can substantially increase sediment delivery. The proportionate increase in DOC, total dissolved nitrogen (TDN) and solute fluxes with runoff has important implications for the anticipated increase of summer rainfall in the Arctic.