The configuration of Smith River estuary in 1850 developed after sea level increased to its present elevation. Sea level was increasing steadily until 3000 to 6000 years ago when it stabilized within five meters of its present elevation (Burke personal communication 1996). In geologic time scales, the Smith River estuary is a very recent structure.

Historic accounts of lower main channels of coastal rivers in the Pacific Northwest describe large networks of sloughs, beaver ponds, driftwood dams, swamps, and grass marshes. Large woody debris in rivers was much more abundant prior to white settlement. Flooding was frequent due to beaver dams, accumulated sediment, fallen trees, and living vegetation in the channels. In addition, interaction between rivers and floodplains was much greater than at present. To illustrate, reports indicate that 5,500 instream trees were removed from a fifty mile stretch of the Willamette River in Oregon. These logs had diameters of five to nine feet and were from 90 to 120 feet long. Lower main channels of some rivers were completely impassable due to driftwood. One particularly large driftwood jam on the Skagit River covered about 120 acres (Sedell et al. 1988).

The Smith River and estuary probably featured similar conditions prior to major human modifications. Although the following description of the estuary from 1881 (Bledsoe 1881) probably occurred after some modifications, it describes an estuary with a complex configuration that contrasts with the present estuary. "Near [the mouth of Smith’s River] are a number of sloughs, branching out from right and left." "Sloughs... branch out from the river on either side, and form a network of safe harbors in which logs could be confined. ...There is very little current in the sloughs even during the highest freshets." "A smooth level beach affords excellent facilities for hauling seines, and ...there are no rapid currents or obstructing drifts." In addition to the network of sloughs, it is likely that the estuary also featured larger accumulations of large woody debris, higher habitat diversity, and higher instream cover complexity.

The estuary and lower river were modified to serve various human needs, including navigation, transportation, logging, and agriculture. Eventually these modifications included channelizing, diking, removing woody debris, and possibly dredging. Channels of some lower tributaries were conceivably used as log haul ways. Levees were constructed and riparian forests were removed. Floods in 1955 and 1964 reportedly decreased pool depths in larger streams and the estuary. The overall result of these changes is a great reduction in habitat complexity in the lower river and estuary (McCain et al. 1995). It appears that there has been a great loss of connectivity between Rowdy Creek and the estuary.

In the lower river, it is suspected that the abundance of gravel has increased since European-American settlement. Gravel mining in the lower Smith River has supplied most of the gravel for Del Norte County. Years ago, gravel mining was advocated for reducing aggradation and thereby increasing access for migrating adult salmonids (California Department of Fish and Game 1980). Aggradation and gravel mining has probably altered spawning habitat in the lower river but long-term benefits or impacts on fish have not been determined.

Levees upstream from the "cattle crossing" restrict the lower Smith River from flowing onto its former flood plain. The levees restrict the width of the channel, increase water velocity, and influence bedload transport rates. This may result in transportation of greater quantities of cobbles into the estuary The levees are also directing the erosive force of peak flows onto the coastal sand dunes. It is possible that the river will erode through the sand dunes to create a new mouth south of the existing mouth. The rate of sand dune formation may or may not be sufficient to outpace erosion by the river. In 1942 and 1966, the Smith River had two outlets into the ocean: the present northern mouth and a southern mouth (USFS aerial photograph, USGS 1966). In 1966, the southern opening to the ocean was located about 0.7 miles (1.1 km) from the northern mouth.

Levees and flood gates along the estuary block tidal waters from entering the sloughs. Former tidal flats are now primarily hay fields and pastures. This has reduced the abundance of tidal eel grass beds that provide rearing habitat for juvenile anadromous salmonids. Because the levees prevent tides from flowing into many areas, they reduce the volume of water moving in and out of the estuary. Prior to construction of the levees, the larger volume of tidal flow created a stronger scouring action. Tidal scouring presumably helped maintain the deep pools that reportedly existed in the estuary. Now the scouring effect of tidal action has been reduced and is evidently insufficient to recreate deep pools and channels in the estuary. Artificial recreation of deep channels is an option. However because scouring effect has been reduced, it is an open question whether the channels would simply fill in again over time. A hydrologic model of the estuary might clarify this question. Perhaps partial restoration of the estuary would be sufficient to recreate tidal scouring.

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