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Scientific Investigations Report 2012–5017

Geomorphic Setting, Aquatic Habitat, and Water-Quality Conditions of the Molalla River, Oregon, 2009–10


The Molalla River in northwestern Oregon is a tributary of the Willamette River, joining the Willamette River about 15 kilometers (km) upstream of Oregon City (fig. 1). The Molalla River is valued for many attributes, including its runs of winter steelhead and spring Chinook salmon, high-quality drinking water, and, in summer, refreshing swimming holes. The Molalla River basin also is home to numerous species of wildlife, including more than 80 species of mammals and 150 species of birds (Alan Gallagher, Molalla River Improvement District, written commun., 2011). The upper Molalla River starts in the Cascade Range foothills, in the Table Rock National Wilderness, in an area surrounded by national forests and private forestland. From vantage points such as U.S. Forest Service (USFS) watchtowers and natural mesas, one can view the surrounding countryside of green forests intersected by deep canyons. The recent Congressional nomination of the upper 35 km of the Molalla River and the Table Rock Fork Molalla River for Wild and Scenic River status is testament to the river’s uniqueness with spectacular views, interesting geology, and opportunities for camping, hiking, trout and salmon fishing, wildlife viewing, and whitewater kayaking (Heyn and Bassett, 2009).

Located between the Clackamas River to the north and the Pudding River to the southwest, the 79-km long Molalla River drains a 900-km2 basin at elevations from 21 m to about 1,510 m (4,940 ft). Stream slope averages 0.0120 m/m in the upper basin and 0.0025 m/m in the lower basin (Bureau of Land Management and U.S. Forest Service, 1999). Nevertheless, with its headwaters located in the rain-snow transition area, and as one of the few free-flowing unregulated rivers in the Pacific Northwest, the Molalla River is susceptible to large rain and rain-on-snow events that produce large peak-flow discharges. Although peak flows are commonly important in forming and maintaining fish habitat, these large events can also cause landslides in the catchment, deliver sediment to the river, erode banks, scour fish spawning areas, and damage roads and homes. Areas just to the south of Canby that are susceptible to flooding include South Alder Creek Lane, South Vale Garden Road, the housing project on South Elm Street, and certain areas near Highway 99E and Canby Grove (Alan Gallagher, Molalla River Improvement District, written commun., 2011).

Observations of gravel bars, infilling of meanders, and channel scars filled with sediment indicate that bedload transport by the Molalla River can be substantial, but it is unclear to what degree sediment input from upstream land-use activities may influence sedimentation in the main-stem river and potential reductions in flood-conveyance capacity of the channel. No comprehensive analysis has been completed that documents the geomorphic setting of the Molalla River or describes the historical and contemporary trends in river-channel position or character over time. Cole (2002) reported on a few aspects of the geomorphic nature of the river at six locations extending up the Molalla River to the Table Rock Fork Molalla River and found downward trends (in a downstream direction) in percentages of large substrate, erosional habitat, and percent canopy cover, and upward trends in fine-grained sediment in the channel and percent substrate embeddedness (degree of sediment infilling around riffle cobbles). Later, Cole and others (2004) reported on channel confinement, gradient, stream substrate, widths, and depths in the main-stem Molalla River. The geomorphic character of the river has potential to adversely affect aquatic life through, for example, channel widening or other processes that deliver sediment, so understanding the dependencies between the health of the aquatic life and the physical setting is needed for integrated and adaptive management of the river as an ecological resource. 

One of the information needs identified by Cole and others (2004) was a field-based survey of the channel geomorphology and channel habitat types in the main-stem river that would collect baseline data on existing conditions. Additionally, concerns about the health of fish populations and declining fish runs have generated interest in documenting the current status of the aquatic habitat available for fish and water-quality conditions in the river. To address these issues, the Molalla River Improvement District, Molalla River Watch, Oregon Department of Fish and Wildlife, and others requested that the U.S. Geological Survey (USGS) conduct a geomorphic and aquatic habitat survey in the lower river. 

The objectives of this study were to (1) complete a geomorphic and aquatic habitat characterization of the lower Molalla River to understand the factors driving current conditions in the river; (2) characterize the water quality, benthic algae, and invertebrate conditions; and (3) evaluate potential interactions between algal assemblages and the geomorphic and water-quality parameters. In addition, given ongoing concerns about potential nutrient enrichment, bacteria, proliferations of nuisance algae in the river, and impacts on water quality such as low levels of dissolved oxygen (DO) and high pH, this study also included two surveys of algal conditions to document the current biomass levels and species composition in the lower river during summer. Because of the often strong control that benthic invertebrate grazing can have on algal populations and their importance as a food resource for fish, qualitative surveys for benthic invertebrates were also conducted during algal sampling. 

Purpose and Scope 

In this report, the results of the analyses of geomorphic conditions and aquatic habitat of the lower Molalla River are presented, including the current conditions and a review of available data and historical photographs to assess changes in the channel width and position over time. This information is used to identify the primary geomorphic controls on channel form. The geomorphic data were combined with the water-quality data to determine if a correlation existed between physical and biological factors and conditions in the river system. Interpretation from this study can be used to complement data and information collected previously by others to inform future research, develop action plans to guide stream-restoration activities, lead management strategies to improve aquatic habitat and water-quality conditions, and possibly reduce the frequency or severity of flooding. 

River Centerline and Geomorphic
Flood-Plain Convention

Analyses in the study were facilitated by the use of two coordinate systems: (1) a river centerline that follows the low-flow channel water surface, thereby enabling description of variables along the primary river flow path and (2) a stationing system based on the geomorphic flood plain that is invariant over the historical time frame and allows comparison of variables independent of the location of the active channel. When describing the right or left bank of the river or the flood plain, the perspective of the observer is as if looking downstream.

Longitudinal location, or stationing, along the river using the river-centerline coordinate system is expressed as a river kilometer (Rkm) distance upstream of the confluence of the Molalla River with the Willamette River (fig. 2; table 1). Because one goal of delineating the river centerline was to generate an approximate longitudinal water-surface elevation profile throughout the study reach, the river centerline was drawn along the path of minimum elevation of the river channel in a digital elevation model generated with airborne light detection and ranging (LiDAR) data. This path was assumed to best represent the flow path of the river at the time of the LiDAR flights. The LiDAR data, collected on different dates from 2007 through early 2009 and discussed in detail later in this report, were available for most of the study area. Where LiDAR data were not available, aerial imagery collected on June 23, 2009, and discussed in detail later in this report, was used to construct the river centerline to the upper extent of the study area at Glen Avon Bridge. 

Longitudinal location along the river corridor using a geomorphic flood-plain coordinate system is expressed as a geomorphic flood-plain kilometer (FPkm) distance upstream of the confluence of the Molalla River with the Willamette River (fig. 2; table 1). The geomorphic flood plain was delineated using methodology developed by O’Connor and others (2003). A combination of LiDAR data, soil maps (Soil Survey Staff, 2008), and Quaternary geologic maps (O’Connor and others, 2001) was examined to identify and delineate the region modified by the river during the recent (Holocene epoch, which encompasses approximately the past 10,000 years) climatic regime. A centerline drawn along the center of the geomorphic flood plain from the upper extent of the study area to the Molalla River’s confluence with the Willamette River and transects drawn orthogonally to the geomorphic flood-plain centerline define the FPkm coordinate system (fig. 2). The geomorphic flood plain used herein should not be considered a regulatory flood plain, and has no relation to existing regulatory flood-plain maps or regional channel-migration mapping. The relation between the river and geomorphic flood-plain coordinate systems, and the relation between these two coordinate systems and river mile (RM) convention available as tick marks on USGS topographic maps, are shown in table 1.

Study Area and Sampling Locations

The study area included the portion of the Molalla River from about the Glen Avon Bridge, located just upstream of the confluence of the Molalla River with the North Fork Molalla River, downstream to the confluence with the Willamette River near Canby (fig. 1). Field data for the study were collected at several sites during a series of float trips down the river corridor as well as at specific sampling locations along the river. The location of the point-specific data-sampling sites for this study is shown relative to Rkm and FPkm stationing in figure 3. The specific type and timing of data collected at each sampling site are listed in table 2. Methodological details of the data collection for the study are discussed in the analysis section of the report.

First posted February 29, 2012

For additional information contact:
Director, Oregon Water Science Center
U.S. Geological Survey
2130 SW 5th Avenue
Portland, Oregon 97201

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