Evaluation of the chemical characteristics of a river system is a fundamental objective when assessing the ecological condition of a watershed. The chemical attributes of a river will not only affect designated uses established for the water resource (e.g. domestic, recreational, agricultural), but they will also influence what biotic assemblages inhabit stream reaches. Additionally, monitoring chemical characteristics along a stream can help identify impaired reaches and possible stressors, as well as monitor the effectiveness of restoration efforts.

Friends of Deer Creek/Sierra Streams Institute has been collecting and analyzing chemical water quality data since 2000 at more than a dozen sites in the Deer Creek watershed. A majority of the chemical data is collected in association with our citizen-based monthly water quality monitoring program.

We are monitoring the following water-quality parameters for Deer Creek:

• Turbidity. Turbidity is a measure of the amount of suspended particles in water. High turbidity is deleterious to many aquatic organisms and indicates excessive erosion in the watershed.
• Conductivity. Conductivity provides an estimate of the amount of salts dissolved in a water body. While some salt content is beneficial, high levels are harmful. An increase in conductivity beyond normal levels may indicate pollution from agricultural runoff or other sources.
• pH. pH is a measure of hydrogen ion concentration and indicates the relative acidity or alkalinity of water. pH significantly higher or lower than the neutral value of 7 is deleterious to most aquatic life. pH measurements outside of a certain range may indicate problems such as excessive decay of organic matter (eutrophication) or acid mine drainage.
• Nitrate (NO3). High nitrate content, typically from wastewater plant discharge and agricultural runoff, is problematic because it stimulates planktonic and algal growth, which can lead to eutrophication.
• Phosphate (PO4). Phosphate is similar to nitrate in terms of sources and effects.
• Dissolved oxygen. Oxygen is necessary for all forms of life. As dissolved oxygen levels in water drop below 5.0 mg/l, aquatic life is put under stress. Dissolved oxygen is reduced when excessive bacterial growth uses up the available oxygen.
• Total Coliform and E. coli bacteria. The concentrations of these indicator organisms can be used to assess the level of bacteria contamination in local waterways and the potential risk to humans recreating in these waterways.
• Water temperature. This is one of the most important parameters because of its influence on other water chemistry parameters such as dissolved oxygen levels, pH, rates of nutrient cycling, and contaminant transformation rates. Water temperature also regulates many aquatic organism functions including growth, reproduction, development, habitat preference, and competition.

Data for all these parameters are presented in several forms below.

Benthic macroinvertebrates (BMI) are excellent biological indicators of ecological condition and function. They are widespread in river systems, long-lived, relatively sedentary, low on the food chain, and in some cases highly sensitive to pollution. These characteristics make BMI ideal "bio-sentinels" for assessing stream health as they can reflect long- and short-term effects of activities within the watershed and specific reaches. Besides being useful biological indicators of water quality conditions, BMI are an integral part of the food web for fish, amphibians, reptiles, and birds.

Ideally, a watershed will have a rich and diverse BMI framework that reflects natural physical and chemical conditions and maintains ecological stability. To determine the condition of BMI communities, an array of metrics can be examined. Our sampling and identification of benthic macroinvertebrates allow us to calculate a variety of such metrics. Two of the most important are the following indices:

• Sensitive EPT Index. This taxonomic-group-based index is the percent of a sample composed of Ephemeroptera, Plecoptera, and Trichoptera (mayflies, stoneflies, and caddisflies), all of which are highly sensitive to pollution. This index incorporates only the most sensitive EPT families (tolerance values of 0-3), removing the more tolerant Ephemeroptera of the families Baetidae and Heptageniidae (tolerance value 4) and Trichoptera of the family Hydropsychidae (tolerance value 4). This makes the Sensitive EPT Index a great tool for assessing creek health.
• Shredder Index. This functional-group-based index is the percent of the sample that is composed of shredders, organisms that consume coarse organic matter such as leaves. This is a specialized feeding strategy, making these organisms more sensitive to ecological disturbance and pollution than more generalized feeders.

Calculations of these indices for the monitoring sites on Deer Creek are presented in several forms below. In general, the BMI metrics indicate that ecological conditions decline from the headwaters to the lower reaches of Deer Creek. For a discussion of the benthic macroinvertebrate data, see the River Ecology chapter of the 2011 Deer Creek Restoration Plan.

Benthic algae (periphyton) are a major component in a river system's food web, acting as autotrophs that convert the sun's energy into organic molecules through photosynthesis. Because benthic algae are attached to the substrate and are at the beginning of the aquatic food chain, the assemblages present in a particular reach are good indicators of physical, chemical, and biological disturbances that have occurred during the time the algae developed. Excessive algae growth can be an indicator of pollution in a river system and is a concern in the managed waterways of California and the Sierra Nevada. Algal blooms can negatively affect aquatic communities by disrupting dissolved oxygen levels, fixed carbon production, nutrient cycling, pH, food web structures, and health of fish.

Measuring algae density and identifying community structures can help pinpoint ecological stressors such as nutrient loading, elevated water temperatures, land disturbances, and more. Disturbances, modifications, and development (such as riparian zone degradation, altered or diverted flows, agricultural land uses, and urbanization) and presence of a wastewater treatment plant can result in nutrient loading and elevated water temperatures which in turn promote algal growth in streams. On the opposite end of the spectrum, an uncommonly low abundance of algal biomass may indicate toxic conditions in a river system although this could also be due to other factors such as a storm event or heavy grazing.

Sierra Streams has been sampling algae during the summer (primarily June through September) in the Deer Creek watershed since 2003 following the targeted riffle approach outlined in the stream periphyton monitoring manual (Biggs and Kilroy, 2000) at 5 sites. Sierra Streams transitioned to the SWAMP reach-wide benthos (RWB) method and expanded its sampling in 2010. This new protocol couples algae and BMI sampling to provide a more robust and comparable dataset for determining ecological conditions at our monitoring sites. Monthly summer algae sampling expanded from 5 to 11 sites.

Our data indicate excessive algae growth is most significant at sites 8 and 9 in lower Deer Creek. This excessive growth is likely caused by elevated water temperatures and nutrient loading below the Lake Wildwood reservoir and wastewater treatment plant.

Historically, the Deer Creek watershed provided habitat to numerous fish species including anadromous fish. Chinook salmon and steelhead runs in a quarter mile stretch of Deer Creek upstream of its confluence with the Yuba River during the fall and winter months were an important resource that helped sustain life for the native peoples of this region. Thompson and West (1880) reported that salmon, brook trout, lake trout, perch, white fish, sucker, chub, and eels were present in Nevada County at the time of the influx of gold miners. Freshwater species native to Deer Creek include the Sacramento sucker, Sacramento pike-minnow, and rainbow trout. The Department of Fish and Game periodically stocks Deer Creek with fish, and fish stocking has occurred in Scotts Flat reservoir as recently as 2010. At present there are numerous non-native fish species in Deer Creek.

Sierra Streams, in collaboration with UC Davis scientists, conducted electro-shocking fish surveys in the Deer Creek watershed during the summer of 2007 and 2008. Data included fish species counts, length, volume, electro-shocking time, water temperature, and stream flow. These data have provided us with insight into what types of fish currently inhabit Deer Creek and its major tributaries.

Currently, fish species downstream of Lake Wildwood Reservoir in Deer Creek during the summer months are characterized by native and non-native warm water species, including Sacramento sucker, redear sunfish, white catfish, Sacramento pike-minnow, spotted bass, and smallmouth bass. Fish shocking data suggest that Deer Creek Falls, a set of steep waterfalls, could serve as a boundary between warm and cold-water fish species. Warm water species were not observed upstream of this location in Deer Creek or its tributaries during the 2007 and 2008 surveys. Upstream of Deer Creek Falls fish shocking data indicate that rainbow and brown trout are the two dominant species in Deer Creek and its tributaries, with redear sunfish present in some locations.

A quarter-mile stretch of Deer Creek from the confluence with the Yuba River, upstream to a point below a steep waterfall known as "Salmon Circle," is utilized by salmon from late fall through spring. The mouth of Deer Creek was once an exceptionally rich salmon and steelhead habitat for the Yuba River; now it is even more critical because Deer Creek is last tributary on the Yuba River before the impassible Englebright Dam. Salmon and steelhead were present on Deer Creek and Squirrel Creek in large numbers in the early part of the 20th century. Steelhead were observed in the 1960s in the first quarter mile of Deer Creek, until the impassible falls, and salmon were observed in large numbers in the 1920s. However, Lake Wildwood reservoir dam on Deer Creek, constructed in 1970, blocks the downstream movement of gravel that is essential for fish spawning habitat. Chinook salmon continue to spawn in Deer Creek but would potentially benefit from in-stream work, such as gravel augmentation and spawning bed enhancement. Sierra Streams is currently engaged in this restoration work. To learn more, follow the link in the Active Project box below.

Sierra Streams staff members perform two types of physical habitat assessments. One type of assessment follows the protocols of the California Stream Bioassessment Procedure (CSBP), the other follows the protocols of the Surface Water Ambient Monitoring Program (SWAMP). Physical habitat assessment is done in conjunction with benthic macroinvertebrate sampling in June and October and is designed to augment the biological sample collection and water quality measurements. Physical habitat data can be used to classify stream reaches and to explain anomalies that might occur in the benthic macroinvertebrate data.

The CSBP protocol calls for the assessment of 10 separate habitat parameters at each sampling reach. These parameters include availability of epifaunal substrates (such as submerged logs) and fish cover, embeddedness of cobbles and boulders, variety of velocity and depth regimes, amount of sediment deposition, degree of channel alteration, stability of banks, and width of the riparian zone vegetation. To learn more about the CSBP, visit the CSBP page of the Aquatic Bioassessment Laboratory site (part of the California Department of Fish and Game).

The SWAMP protocol calls for the assessment of similar habitat parameters (12 total) along 11 cross-sectional transects distributed evenly along a reach, which varies between 150 and 120 meters in length depending on stream width. These parameters include wetted width, flow habitat delineation, slope, sinuosity, canopy cover, in-stream habitat, and bank stability. To learn more about the SWAMP protocol and program, visit the program's home page.

Geomorphological surveys involve collecting data that describe a stream's physical characteristics. In our geomorph surveys, we collect three types of data:

• Pebble counts. Pebble counts provide representative samples of the bedload particle distribution, which is an important determinant of habitat suitability for fish and other aquatic organisms.
• Longitudinal profile. A longitudinal profile is a representation of water surface and bed elevation along a reach of a stream. It provides important information about a stream's flow characteristics and flow habitat types (e.g., location and size of pools and riffles). A profile also indicates which process--transport or deposition--dominates in a reach.
• Stream channel cross section. A cross section provides important information about channel geometry, and helps determine how a stream's longitudinal profile influences its flow characteristics. Cross-sectional data can indicate stream degradation, especially when cross-sections from the same location are compared over time.

At each site, we conduct three or four pebble counts, construct three or four cross sections, and construct a single longitudinal profile. This protocol is reflected in the spreadsheet data listed below.

Geomorphic studies are important because they identify key characteristics of physical stream processes and channel structure that shape how ecological communities develop and function. Quantifying and documenting geomorphic conditions and processes is a critical part of identifying factors that may maintain, enhance, or limit ecological processes in riverine systems. Geomorphic data also provide a foundation from which to design and evaluate river restoration projects.

Pebble counts, for example, tell us a great deal about whether a stream provides good habitat for fish. Chinook salmon require a specific range of material (pebbles) for their in-stream habitat. If it is too large they cannot mobilize the material to create their spawning beds; if it is too small there might not be enough oxygen/nutrient flow into the spawning bed.  By conducting pebble counts we can determine whether or not the current in-stream habitat is suitable for Chinook salmon. If not, this points to the need for restoration.

Want to know more? Faculty in the Geology Department at the University of Wisconsin, Stevens Point have put together an online text with an excellent chapter on fluvial systems.

Sierra Streams Institute measures stream flow at nine sites on Deer Creek and its tributaries as part of a larger Sierra Water Trust project funded by the US Environmental Protection Agency and administered by American Rivers and the Natural Heritage Institute. For more information about the Sierra Water Trust project and to access stream flow data, please follow the link in the Acive Project box below.

Sierra Streams monitors several sites during storm events to evaluate how elevated flows affect mercury and sediment loads and chemical parameters such as water temperature, pH, and specific conductivity. Examining high flow periods is a critical component in determining the condition of the Deer Creek watershed, as transport of sediment, nutrients, algae, bacteria, and heavy metals often increases during these flow pulses.