Description of Molalla River Basin


An understanding of the underlying geology, hydrology, and aquatic ecology of the Molalla River basin was critical to achieving the objectives of this study. Those characteristics of the basin are summarized below and are described in more detail in the watershed assessments by the Bureau of Land Management and U.S. Forest Service (1999) and Cole and others (2004).


Geology


The Molalla River flows westward from the Cascade Range into the Willamette Valley, a broad geographic region bounded by the Cascade Range to the east and the Oregon Coast Range to the west that has been topographically low since about 20 million years ago (Hampton, 1973). The Willamette Valley was filled with the Columbia River Basalt Group by about 15 million years ago and subsequently defined by continued uplift to the east and west along a north-south trending syncline (Hampton, 1972; Gannett and Caldwell, 1998). This topographic depression was subsequently filled to its current surface with as much as several hundred meters of alluvium eroded from neighboring mountain ranges and from the Columbia Plateau by late-Pleistocene Missoula Flood sediments (O’Connor and others, 2001). 


The Cascade Range is subdivided into two distinct geologic regions. To the east, the Oregon High Cascades is topographically higher, with relatively gentle slopes, little dissection, and permeable bedrock that holds groundwater (Jefferson and others, 2006). To the west, the Western Cascade Range, a predominantly igneous complex assemblage consisting of andesite and basalts interspersed with pyroclastic layers, is geologically older and more deeply dissected (Gannett and Caldwell, 1998) and less permeable than the Oregon High Cascades. In contrast to its neighbors to the north and south that drain the Oregon High Cascades (Clackamas and North Santiam Rivers), the Molalla River heads almost exclusively in the Western Cascade Range.


Volcanism associated with the subduction of the Juan de Fuca plate under the North American plate built the base units of the Western Cascade Range until about 35 million years ago, when the focus of volcanic activity shifted eastward to the Oregon High Cascades (Gannett and Caldwell, 1998). The upper canyon reaches of the Molalla River study area (upstream of about FPkm 29, fig. 3) lie between upland hills of Miocene and Oligocene andesite and breccias, and the river flows through a narrow bedrock corridor of Pleistocene alluvial deposits (Gannett and Caldwell, 1998) that restricts channel movement (see photographs 1 and 2). These Pleistocene deposits consist of interlayered units of conglomerate and sandstone created by fluvial (cobble and gravel layering) as well as lahar (volcanic debris flow) deposition from drainage networks emanating from the Western Cascade Range. These fluvial deposits seem to correlate with periods of active Cascade Range glaciation during the Pleistocene (Clark and Bartlein, 1995; O’Connor and others, 2001). Between FPkms 20 and 29, the river flows across a flood plain of late-Pleistocene and Holocene alluvial fill bounded by Pliocene and Miocene sedimentary bedrock hills (Gannett and Caldwell, 1998). Downstream of FPkm 20, the Molalla River enters the broad alluvial plain of the Willamette Valley that cuts across high terraces of Missoula Flood sediment deposited during the late Pleistocene (O’Connor and others, 2001).


Between 15,000 and 20,000 years ago, 60 to 90 megafloods (O’Connor and Benito, 2009) burst from ice-sheet-dammed Lake Missoula in northern Montana and flowed across eastern and central Washington, and then followed the course of the lower Columbia River valley to the sea (Bretz, 1925; Baker, 1973). As these floodwaters debouched from the Columbia River Gorge, a hydraulic constriction downstream of Portland, Oregon, impounded flow to an elevation at least 150 m above sea level (O’Connor and others, 2001). At least 40 floods, primarily between 12,700 and 15,000 years ago (O’Connor and others, 2001), backed up to the upland hills bounding the southern edge of the Portland Basin and spilled into the Willamette Valley, depositing sediment over the region of the present-day Molalla River flood plain. The post-Pleistocene Molalla River incised into these Missoula Flood deposits to the base level set by the Willamette River and established the contemporary geomorphic flood plain (fig. 2). The Missoula Floods entered the Willamette Valley through two low divides: the Oregon City gap to the east and the Rock Creek gap to the west (O’Connor and others, 2001). Flood waters that poured through the Oregon City gap (fig. 1), located along the course of the Willamette River between Oregon City and Canby, created a broad, spreading alluvial fan of coarse-grained sediment, on top of which the City of Canby is built. This coarse-grained deposit bounds the northern and eastern portions of the Molalla River geomorphic flood plain between FPkms 10 and 2. Similarly, flood waters poured through the Rock Creek gap (fig. 1) to deposit a coarse-grained fan to the west of Canby (O’Connor and others, 2001). This fan bounds the western edge of the geomorphic flood plain from FPkm 1 to FPkm 4. Fine-grained deposits from the Missoula Floods extend south from Canby, filling much of the Willamette Valley with a thick mantle of sand, silt, and clay (O’Connor and others, 2001). The topographically high terrace that bounds the geomorphic flood plain from FPkm 4 to FPkm 12 is capped by this finer-grained Missoula Flood sediment. 


Hydrology


The flow of the Molalla River is unregulated; however, there are numerous diversions for agriculture and other uses. The major tributary systems to the lower river are the Milk Creek basin, which enters the river from the north, and the Pudding River, which enters just upstream of the confluence with the Willamette (fig. 3). Climate in the Molalla River basin is characterized by warm and dry summers while the winters are wet and mild at lower elevations with cool temperatures.


The USGS currently operates one streamflow-gaging station upstream of Canby (station No. 14200000; Molalla River near Canby, Oregon). This gaging station has been operated discontinuously since 1928, with a total of 56 years of record (1928–59; 1963–78; and 2000-present); rainfall has been recorded at this gaging station since 2001. From 1936 to 1992, the USGS also operated a streamflow-gaging station on the Molalla River above Pine Creek near Wilhoit, Oregon (14198500). The mean monthly precipitation and discharge measured near Canby, Oregon, are shown in figure 4. Precipitation data were averaged from water year 2001 to 2010. On average, the largest monthly discharge, 69 m³/s (2,420 ft³/s), occurs in January and the smallest monthly discharge, 2.9 m³/s (102 ft³/s), occurs in August. The long-term average of minimum daily discharges is 1.7 m³/s (60 ft³/s); the lowest recorded daily flow was 0.6 m³/s (22 ft³/s) in 1959. Eighty percent of the flow of the Molalla River and 73 percent of the precipitation in the basin occurs between November and April (Bureau of Land Management and U.S. Forest Service, 1999). The short lag time between precipitation and runoff is indicative of the peak flow being rainfall dominated. The upper catchment of the Molalla River basin originates in the Western Cascade Range, a relatively steep, deeply dissected range that, compared to other streams in the Cascade Range, tends to be runoff dominated (Jefferson and others, 2006). The lack of water storage in (and later release from) either a seasonal snowpack or groundwater in the upper catchment contributes to low summer flows (Conlon and others, 2005) and warm stream temperature in summer (Jefferson and others, 2004). 


The Molalla River watershed commonly receives heavy winter rain associated with atmospheric moisture that originates in the tropics (Cooper, 2005). The runoff from these storms can combine with meltwater from antecedent snow cover to create extreme high flows. Examples of such high-flow events on the Molalla River include peak flows of 1974, 1996, and the December 1964 storm, often referred to as the Christmas Flood (Hubbard, 1991; Taylor and Hatton, 1999). The 10 largest peak flow events on record have all occurred between the months of November and March.


To estimate annual peak flows for the Molalla River near Canby during years the Canby gaging station was not in operation, data from the Molalla River near Wilhoit gaging station (14198500), located at Rkm 54, and from the Clackamas River gaging station (14210000; Clackamas River at Estacada, Oregon) were used in a regression analysis of log-transformed peak-flow data. Using the annual peak-flow data from the Clackamas River gaging station (Q_Clackamas), the estimated peak flow at Canby, (Q_Canby), is given as:


log (Q_Canby) = 0.76 log (Q_Clackamas) + 0.80, 


yielding a coefficient of determination of R² = 0.73. Similarly, using the annual peak-flow data from the Molalla River near Wilhoit gaging station (Q_Wilhoit), the estimated peak flow at Canby, (Q_Canby), is given as:


log (Q_Canby) = 0.90 log (Q_Wilhoit) + 0.68, 


yielding a coefficient of determination of R² = 0.85. The regression estimates made on the basis of data from the Clackamas and Wilhoit gaging stations have a standard error of 80 m³/s (2,800 ft³/s) and 70 m³/s (2,400 ft³/s), respectively. Table 3 summarizes the data used to create an enhanced peak discharge record for the Molalla River near Canby for the period 1909 to 2009.


Peak flows, reconstructed in this manner, have varied between 92 m³/s (3,250 ft³/s) and 1,240 m³/s (43,600 ft³/s) between 1909 and 2009 (fig. 5). During the overlapping years of record for the two gaging stations, the estimated flows from the regression equations are plotted showing the approach reasonably approximates peak flows for those years not directly gaged. The largest peak of record on the Molalla River occurred December 22, 1964, with a measured discharge of 1,240 m³/s (43,600 ft³/s). This discharge produced a large flood and widespread channel changes. Other large peak flows include 1,030 m³/s (36,200 ft³/s) in 1972 and 883 m³/s (31,200 ft³/s) in 1974; both events were recorded at the USGS gaging stations. Since the Canby gaging station was reactivated in 2000, the largest peak flow was 691 m³/s (24,400 ft³/s), on January 2, 2009. In the past 30 years, the largest peak flow occurred on February 2, 1996, when the gaging station at Canby was not operating. Stage height at the Canby gaging station location for this 1996 high-flow event was recorded to be 7.50 m by the Canby Fire Department (Andy Bryant, National Weather Service, written commun., 2010). Although a verified stage-discharge relation to estimate discharge for the February 1996 event is not available, application of the current stage-discharge relation to this record stage would result in a discharge estimate of about 900 m³/s (32,000 ft³/s) for the 1996 peak event.


Using the Canby gaging record, a log-Pearson Type III (LP3) distribution was created (U.S. Geological Survey, 1981) to calculate recurrence-interval events and annual exceedance probability of peak discharge on the Molalla River (table 4). 


Designated Beneficial Uses and Status of Fish Populations


Designated beneficial uses for the Molalla River include water for drinking, irrigation, and livestock; anadromous fish passage, spawning, and rearing; habitat for resident fish and aquatic life; fishing; boating; water contact recreation; and hydropower (Oregon Administrative Rules, Chapter 340, Division 41, Rule Number 340-41-0340). The Molalla River currently supports salmon and steelhead runs in varying abundances each year, although native stocks of salmonids are reduced from historical numbers, a consequence of a combination of several factors, including habitat degradation, heavy fishing pressure, reduced ocean survival, and competition with hatchery fish (Oregon Department of Fish and Wildlife, 1992; Bureau of Land Management and U.S. Forest Service, 1999). The lower reaches of the Molalla River are used by nonnative fall Chinook salmon and the upper, higher gradient reaches are used by native winter steelhead and spring Chinook (Oregon Department of Fish and Wildlife, 1992). The spring Chinook and winter steelhead are part of the Upper Willamette Evolutionary Significant Units that were federally listed as threatened under the Endangered Species Act in 1999, and reaffirmed in 2005 for spring Chinook and in 2006 for winter steelhead (National Atmospheric and Oceanic Administration Fisheries, 2005; 2006). The extinction risk for spring Chinook salmon in the Molalla River is considered high, whereas winter steelhead runs are at lesser risk (Oregon Department of Fish and Wildlife and National Atmospheric and Oceanographic Administration Fisheries, 2010). The Molalla River and some of its tributaries also provide habitat for summer steelhead, fall Chinook salmon, coho salmon, and resident cutthroat trout (McIntosh and others, 1990).


Aquatic Habitat and Water Quality Conditions


The quality of aquatic habitats in the Molalla River, including riffle spawning areas, pool frequency and depth, channel complexity, and the amount of large wood is critical for resident and anadromous fish. High-quality aquatic habitats are also necessary for supporting benthic invertebrate populations that are important components of river food webs that support salmonid fishes. 


Aquatic habitat quality in the Molalla River basin is variously affected by anthropogenic activities in the basin and along the river and its flood plain. Logging practices, including construction of splash dams and log drives, once scoured streambeds and fish spawning areas. Later, commercial timber harvesting and road construction probably increased sediment loading to the river that degraded habitat and increased turbidity (Bureau of Land Management and U.S. Forest Service, 1999). In 1999, the Bureau of Land Management (BLM) watershed analysis concluded that instream habitat conditions in the upper Molalla River basin upstream of Feyrer Park Road are generally fair to good in the main stem and poor to fair in most of the tributaries surveyed, based on pool frequency and size, percent secondary channels, and wood volume (Bureau of Land Management and U.S. Forest Service, 1999). The primary impacts in the upper basin include sedimentation, partly due to landslides, and lack of instream wood. Wood serves to create and maintain complex habitats, increases the retention of spawning gravel and nutrients, reduces the velocity of high flows, and creates refuge areas for juvenile and adult fish. The watershed analysis also concluded that conditions in the upper basin should improve as timber harvest units revegetate and stabilize.


In many reaches of the Molalla River, high-quality habitat exists for fish and other aquatic life, including highly productive riffles, braided channels with side channels, and relatively deep holding pools. During summer, however, some of the habitat is marginalized due to the low streamflows that contribute to high water temperatures. Some stretches of the lower river contain large rafts of wood and log jams, but much of the wood is perched at the heads of gravel bars, out of the water and inaccessible to fish. Channelization and bank stabilization projects also have the potential to impact habitat for fish by increasing water velocities or restricting access to side channels, for example, which are important refuges for fish during high flows.


Water quality is also critically important for fish that inhabit the Molalla River, and previous studies (Oregon Department of Environmental Quality, 1988; Bureau of Land Management and U.S. Forest Service, 1999; Williams and Bloom, 2008) have documented the occurrence of several water-quality issues including high water temperatures, elevated levels of bacteria and sediment, and low concentrations of dissolved oxygen associated with nutrient enrichment and growths of attached benthic algae (periphyton). Although water temperatures are problematic throughout most of the river, nutrient, algae, and dissolved oxygen conditions are most severe in the lower reaches of the river, downstream of agricultural and urban sources.


Both point and especially non-point source pollution have the potential to negatively affect water quality in the Molalla River. The wastewater facility for the City of Molalla discharges treated effluent to the river downstream of Feyrer Park during the wet season only, typically between November 1 and April 30, and uses managed land application during the dry season (Tetra Tech and KCM, Inc., 2000). Runoff from timber harvest and agricultural areas, as well as from urban areas, also contributes sediment, nutrients, and other pollutants to the river.


The Oregon Department of Environmental Quality (ODEQ) has been monitoring the quality of water in the lower Molalla River several times per year since the early 1980s as part of their ambient monitoring program, and currently collects samples at RM 3 downstream of Knights Bridge. In an early assessment of the Molalla River, ODEQ determined that water quality in the upper basin was affected by inputs of sediment from landslides, forestry, and road related runoff (Oregon Department of Environmental Quality, 1988). Water quality in the middle river, downstream of the town of Molalla, was affected by erosion and turbidity, low levels of dissolved oxygen, sediment, and low-flow problems as a result of water withdrawals (Bureau of Land Management and U.S. Forest Service, 1999). In the lower river, high water temperatures, high biochemical oxygen demand, and low levels of dissolved oxygen have been a problem during summer low-flow periods as a result of non-point source pollution (Cude, 1996). In 1998, the lower Molalla River, from its mouth to the confluence with North Fork Molalla River, was on the 303(d) list of water quality impaired streams for high water temperatures (summer) and E. coli bacteria (autumn-spring). ODEQ also noted that instream water rights were often not met at the Goods Bridge gaging station during summer, so flow modification was listed as contributing to high water temperatures.


The most recent (1998–2007) analysis of the ODEQ data classified water quality at the Knights Bridge site as “good” (score of 89 out of 100), based upon an index that includes water temperature, dissolved oxygen levels, biochemical oxygen demand, pH, and the concentrations of total solids, ammonia, nitrate, total phosphorus, and bacteria (Oregon Department of Environmental Quality, 2008). Nevertheless, several stream reaches of the Molalla River currently do not meet water-quality standards for water temperature and bacteria (Williams and Bloom, 2008). A detailed analysis of data for the temperature Total Maximum Daily Load (TMDL), including Thermal Infrared Radiometry (TIR) data collected in July 2004, found temperatures in the main stem as much as about 26°C (Williams and Bloom, 2008). Heat-source modeling (Boyd and Kasper, 2003) showed that heating resulted from increased solar warming as a consequence of a paucity of streamside vegetation, reduced streamflow, and inputs of relatively warmer water from certain tributaries. Inputs of cooler water from other tributaries such as Table Rock Fork Molalla River, Trout Creek, North Fork Molalla River, Russell Creek, and Milk Creek produces drops in water temperatures in the main stem, but TIR data show downstream temperatures continued to rise until the next tributary downstream provided additional cooler water. Inputs of cold spring water also enter the Molalla River, mainly upstream of Gawley Creek and downstream of the North Fork Molalla River (Williams and Bloom 2008), which probably keep temperatures in the main stem from getting even warmer. 


High water temperatures are stressful for salmonids and favor production of less desirable warm water fish species, some of which are introduced (Oregon Department of Fish and Wildlife, 1992). Oregon Department of Fish and Wildlife found that low summer flows and warm water temperatures were the two most important limiting factors affecting spring Chinook and winter steelhead in the Molalla River (Bureau of Land Management and U.S. Forest Service, 1999). Most (78 percent) of the water use in the Pudding-Molalla River basin is for agriculture, with 7 percent for municipal uses. Although instream flow requirements do exist in the Molalla River for aquatic life and pollution prevention, these tend to be among the most junior water rights (Williams and Bloom 2008).


As required by the Clean Water Act of 1972, and because certain stream reaches of the Molalla Pudding Subbasin were not meeting water-quality standards, ODEQ produced a TMDL and developed a Water-Quality Management Plan (Williams and Bloom, 2008) designed to protect human health, aquatic life, and other designated beneficial uses of the water. In December 2008, the U.S. Environmental Protection Agency approved the TMDL. The plan establishes waste load allocations for point and non-point sources for parameters not currently meeting water-quality standards.


Although the Molalla River is not currently on the 303(d) list for nuisance algae, high pH, or low dissolved oxygen, nutrient enrichment and these associated eutrophication issues have been a concern in the past. Excessive biomass of periphyton algae in the Molalla River and high rates of algal photosynthesis produce supersaturated levels of dissolved oxygen and high pH to levels that could be harmful for fish and other aquatic organisms. Water quality is critically important for humans as well as aquatic life because the cities of Molalla and Canby use the Molalla River for their public drinking-water supply. Excessive amounts of algae can affect water supplies by clogging intakes, producing taste and odor problems, and enriching raw water with organic carbon that can produce toxic disinfection by-products (DBPs) when the water is treated. Although DBPs were once an issue at the Canby drinking-water treatment plant, upgrades to the plant, including elimination of pre-chlorination, greatly reduced levels of DBPs in treated water. Clogging of the intake screens by algae, however, continues to be a problem during the late summer (Brian Hutchins, Canby drinking-water plant facility manager, oral commun., 2011).


Pesticides also have the potential to affect water quality in the Molalla River, although data are limited to just a few samples. In 1994, USGS identified several pesticides in the Molalla River at Knights Bridge, including the herbicides atrazine, simazine, EPTC, and napropamide, and the insecticide chlorpyrifos (USGS NWIS database, http://waterdata.usgs.gov/nwis). The lower three kilometers of the Molalla River are also influenced by the often highly turbid Pudding River, which is currently on the ODEQ’s 303(d) list as water-quality impaired due to high water temperatures, fecal coliform bacteria, and elevated concentrations of legacy insecticides dieldrin and DDT, which are no longer in use (Williams and Bloom, 2008). A previous USGS study by Rinella and Janet (1998) documented high concentrations of sediment, nutrients, and several pesticides in the Pudding River and many of its agricultural tributaries. It is not known how anadromous fish returning to the Molalla River might be affected by exposure to poor water-quality conditions in the affected reach downstream of the Pudding River, or if anadromous fish homing behavior is disrupted by exposure to pesticides (Scholz and others, 2000).


Land Use and Anthropogenic Impacts


Forest management and road construction in the upper basin, and agriculture, gravel mining, urban development, and other activities in the lower basin all have the potential to affect the landscape, aquatic habitat, and water quality of the Molalla River (Bureau of Land Management and U.S. Forest Service, 1999; Cole and others, 2004). Although Federal lands owned by the BLM and USFS comprise about 35 percent of the basin, 53 percent is private industrial forestland, and the remaining land is used primarily for agriculture, interspersed by parcels of rural residential, urban, and some industrial land in the lower basin. 


The Molalla River basin has a history of logging dating back to the early 1900s (see review in Cole and others, 2004). Early logging operations used the Molalla River and Milk Creek for transporting logs to mills, and included the use of log ponds, flumes, and splash dams. Some of the early practices were damaging to aquatic ecosystems as logs were skidded through streams and across fish spawning areas. In the early 1940s, 300–600 log trucks per day traveled on the Molalla Forest Road on their way to mills in Molalla (Cole and others, 2004). Widespread road construction and commercial timber harvesting began in the 1950s and 1960s, with harvest occurring down to the river’s edge, which reduced wood recruitment to the river and assemblages of large woody debris in the flood plain (Swanson and Lienkaemper 1978, Likens and Bilby 1982). Today, just 4 percent of the old growth forest remains in the Molalla River basin, much of it in the Table Rock Wilderness (Bureau of Land Management and U.S. Forest Service, 1999). Intensive logging subsided in the 1970s and 1980s, and by the 1990s, most of the timber harvest had shifted to private forestland. 
By 1998, there were over 1,000 km of roads in the Molalla River basin, and the dominant land cover was regeneration forests—open sapling/brush from 10 to 40 years of age and 40 to 80-year-old closed canopy stands. Water Availability Runoff (WAR) hydrologic models have shown that such removal of forest canopy and creation of extensive open areas in the upper Molalla River watershed has resulted in additional snow accumulation that has exacerbated flooding during rain-on-snow events (Bureau of Land Management and U.S. Forest Service, 1999), such as those that occurred in 1964 and 1996. Overall, the BLM’s watershed analysis rated the basin to be in a poor to fair condition, and concluded that aquatic habitat in the upper Molalla River basin was now degraded from decades of forest management, timber harvesting, road building, and stream cleaning, all of which have resulted in a lack of wood in the upper river. In contrast, large accumulations of wood and large log jams are present in the middle and lower Molalla River, where they provide cover for fish and may contribute to migration of the river’s channel. Property damage from historical flooding has, over time, resulted in construction of several bank stabilization projects beginning in 1938 by the U.S. Army Corps of Engineers (USACE), and more recently involving the Natural Resources Conservation Service (NRCS) and other private and public groups. Twenty of these projects have been built within the lower 40 km of the Molalla River (Cole and others, 2004).


First posted February 29, 2012