Skagit River watershed is the largest draining into Puget Sound and has the most extensive glacial cover of any basin > 5,000 km² in the US outside of Alaska. We examined the importance of these glaciers to the basin's summer water balance using an empirical approach. In 1959 approximately 396 glaciers covered 170.23 ± 8.50 km² of the basin. Since then, combined glacier area has decreased by 32.02 ± 1.60 km² (- 19%), with most of the loss between elevations of 1600 m and 2100 m. Fifty years ago surface melting of snow, firn, and ice from Skagit glaciers provided from 0.440 ± 0.055 to 0.742 ± 0.093 km³ of water in summer (May through September) to the Skagit River at Concrete. Today, the surface melt component has decreased (- 24% ± 9%) and now ranges from 0.333 ± 0.042 km³ of water in cool-wet years to 0.559 ± 0.070 km³ in warm-dry years. Surface melt from the remaining glaciers continues to provide 6–12% of the river's total summer runoff, and roughly twice that fraction during August and September. Cold glacial meltwater is concentrated in tributaries Thunder Creek, White Chuck River, Suiattle River, Baker River, and Cascade River. Between 1959 and 2009 average cumulative annual mass balance of five monitored glaciers was -20.35 ± 3.63 m water equivalent. This has resulted in glacial water volume loss of 3.01 ± 0.69 km³ basin-wide, representing the elimination of ∼ 100 years of fresh water supply for Skagit County at the current rate of consumption.

Previous studies have shown that the impacts of climate change on the hydrologic response of the Skagit River are likely to be substantial under natural (i.e. unregulated) conditions. To assess the combined effects of changing natural flow and dam operations that determine impacts to regulated flow, a new integrated daily-time-step reservoir operations model was constructed for the Skagit River Basin. The model was used to simulate current reservoir operating policies for historical flow conditions and for projected flows for the 2040s (2030–2059) and 2080s (2070–2099). The results show that climate change is likely to cause substantial seasonal changes in both natural and regulated flow, with more flow in the winter and spring, and less in summer. Hydropower generation in the basin follows these trends, increasing ( 19%) in the winter/ spring, and decreasing (- 29%) in the summer by the 2080s. The regulated 100-year flood is projected to increase by 23% by the 2040s and 49% by the 2080s. Peak winter sediment loading in December is projected to increase by 335% by the 2080s in response to increasing winter flows, and average annual sediment loading increases from 2.3 to 5.8 teragrams ( 149%) per year by the 2080s. Regulated extreme low flows (7Q10) are projected to decrease by about 30% by the 2080s, but remain well above natural low flows. Both current and proposed alternative flood control operations are shown to be largely ineffective in mitigating increasing flood risks in the lower Skagit due to the distribution of flow in the basin during floods.

Management of extreme low-flows requires fundamental trade-offs between water extraction for human use (e.g. for irrigation and municipal water supply) and in-stream flows to protect aquatic ecosystems. In the context of protecting endangered salmon and other cold-water fish species in small streams, extreme low-flows are one of the most important aspects of the flow regime. We quantify projected changes in low-flow magnitude and timing for several lowland tributaries of the Skagit River basin in response to regional climate change. Ten hydrologic model simulations of mid-21st century (2030–2059) streamflows are compared against a historical period (1917–2006). Each of the hydrologic simulations are forced by atmospheric variables developed from respective CMIP3 global climate model (GCM) output downscaled to 1/16th degree resolution using the Hybrid-Delta downscaling method. Baseline historical simulations are forced by historical gridded meteorological data sets of temperature and precipitation, and additional meteorological variables reconstructed using the MTCLIM weather preprocessor. Hydrologic simulations were performed using the Distributed Hydrology Soil Vegetation Model (DHSVM) implemented at 30–m resolution. Analysis of the DHSVM streamflow simulations projects future low-flows in Skagit lowland tributaries will decrease by 5–20% and low-flow conditions will persist on the order of a week longer into early fall. For the Samish and Nookachamps basins, the projected changes in future low-flow regimes are larger than for the smaller basins included in the study. Projected changes in near-average low-flows are larger and more consistent between different climate change scenarios than are projected changes for the most extreme low-flow events.

Current understanding of the combined effects of sea level rise (SLR), storm surge, and changes in river flooding on near-coastal environments is very limited. This project uses a suite of numerical models to examine the combined effects of projected future climate change on flooding in the Skagit floodplain and estuary. Statistically and dynamically downscaled global climate model scenarios from the ECHAM-5 GCM were used as the climate forcings. Unregulated daily river flows were simulated using the VIC hydrology model, and regulated river flows were simulated using the SkagitSim reservoir operations model. Daily tidal anomalies (TA) were calculated using a regression approach based on ENSO and atmospheric pressure forcing simulated by the WRF regional climate model. A 2-D hydrodynamic model was used to estimate water surface elevations in the Skagit floodplain using resampled hourly hydrographs keyed to regulated daily flood flows produced by the reservoir simulation model, and tide predictions adjusted for SLR and TA. Combining peak annual TA with projected sea level rise, the historical (1970–1999) 100-yr peak high water level is exceeded essentially every year by the 2050s. The combination of projected sea level rise and larger floods by the 2080s yields both increased flood inundation area ( 74%), and increased average water depth ( 25 cm) in the Skagit floodplain during a 100-year flood. Adding sea level rise to the historical FEMA 100-year flood resulted in a 35% increase in inundation area by the 2040's, compared to a 57% increase when both SLR and projected changes in river flow were combined.

Historical aerial photographs, from 1937 to the present, show Skagit Delta tidal marshes prograding into Skagit Bay for most of the record, but the progradation rates have been steadily declining and the marshes have begun to erode in recent decades despite the large suspended sediment load provided by the Skagit River. In an area of the delta isolated from direct riverine sediment supply by anthropogenic blockage of historical distributaries, 0.5-m tall marsh cliffs along with concave marsh profiles indicate wave erosion is contributing to marsh retreat. This is further supported by a “natural experiment” provided by rocky outcrops that shelter high marsh in their lee, while being bounded by 0.5-m lower eroded marsh to windward and on either side. Coastal wetlands with high sediment supply are thought to be resilient to sea level rise, but the case of the Skagit Delta shows this is not necessarily true. A combination of sea level rise and wave-generated erosion may overwhelm sediment supply. Additionally, anthropogenic obstruction of historical distributaries and levee construction along the remaining distributaries likely increase the jet momentum of river discharge, forcing much suspended sediment to bypass the tidal marshes and be exported from Skagit Bay. Adaptive response to the threat of climate change related sea level rise and increased wave frequency or intensity should consider the efficacy of restoring historical distributaries and managed retreat of constrictive river levees to maximize sediment delivery to delta marshes.

Future climate simulations based on the Intergovernmental Panel on Climate Change emissions scenario (A1B) have shown that the Skagit River flow will be affected, which may lead to modification of the estuarine hydrodynamics. There is considerable uncertainty, however, about the extent and magnitude of resulting change, given accompanying sea level rise and site-specific complexities with multiple interconnected basins. To help quantify the future hydrodynamic response, we developed a three-dimensional model of the Skagit River estuary using the Finite Volume Community Ocean Model (FVCOM). The model was set up with localized high-resolution grids in Skagit and Padilla Bay sub-basins within the intermediate-scale FVCOM based model of the Salish Sea (greater Puget Sound and Georgia Basin). Future changes to salinity and annual transport through the basin were examined. The results confirmed the existence of a residual estuarine flow that enters Skagit Bay from Saratoga Passage to the south and exits through Deception Pass. Freshwater from the Skagit River is transported out in the surface layers primarily through Deception Pass and Saratoga Passage, and only a small fraction (∼ 4%) is transported to Padilla Bay. The moderate future perturbations of A1B emissions, corresponding river flow, and sea level rise of 0.48 m examined here result only in small incremental changes to salinity structure and interbasin freshwater distribution and transport. An increase in salinity of ∼1 psu in the near-shore environment and a salinity intrusion of approximately 3 km further upstream is predicted in Skagit River, well downstream of drinking water intakes.