The ongoing removal of the Elwha and Glines Canyon dams on the Elwha River have mobilized a massive amount of sediment that has accumulated and altered habitats throughout the watershed. Accumulation has been particularly high in the estuaries and nearshore, significantly altering physical and biological conditions. We have been measuring a suite of parameters since 2010 to better understand how sediment accumulation and suspended sediment alter physical and biological conditions, and how those changes alter habitat conditions. In estuarine and nearshore habitats we are measuring salinity, temperature, turbidity, primary productivity, light availability, and nutrient concentration. In the estuary we are additionally measuring pH, dissolved oxygen concentration; in the nearshore we are additionally measuring current direction and speed, wave height and direction, and sediment deposition and residence time. Our data show that conditions in the estuary changed from a tidally influenced, brackish estuary to a freshwater estuary that is episodically isolated from the river within one year of dam removal. In addition to the fine sediment that has accumulated in the estuary, this hydrologic change has resulted in ecological changes to the estuary, including a shift in species composition of fish and invertebrates. In the nearshore, light availability has decreased during the dam removal process, and the incidence of seafloor sedimentation has increased, which is ephemeral owing to winnowing from periodic strong currents. Burial, scouring, and reduced light availability caused by increased sedimentation are likely negatively impacting algal communities in the nearshore that are within the Elwha River plume. This study advances our understanding of how the timing and magnitude of sediment delivery affects habitat availability, species persistence, and community composition change with implications to future land-use changes