Scientific Investigations Report 2006–5230
U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2006–5230
PHABSIM investigations were done on six Salmon River tributaries during summer 2005. Data were collected at eight study sites (table 1): one site on lower Big Boulder Creek (BB1), four sites on Challis Creek (CH1, CH2, CH3, and CH4) and two of its perennial tributaries, lower Bear Creek (BE1) and lower Mill Creek (ML1), and one site on lower Morgan Creek (MC1). A plan view of each PHABSIM study site showing locations of specific transects are shown in the appendixes, figs. A1, B1, C1, D1, E1, F1, G1, and H1. Fishery information from Murphy and Yankey (2003a, 2003b) were used to help with selection of study sites on Challis and Morgan Creeks. PHABSIM WUA results are presented for adult and spawning bull trout, Chinook salmon, and steelhead trout for each study site. In addition, WUA results are presented for riffle dwelling invertebrate taxa (Ephemeroptera, Plecoptera, and Trichoptera) for each site. Because of the concerns about PHABSIM modeling results for juveniles, they are not presented in this report. Mulitple passage transects also were evaluated for various depth criteria at each study site.
In addition to instantaneous streamflow data collected at these study sites, continuous streamflow was recorded at USGS streamflow-gaging stations upstream of all diversions on the Salmon River (SRG), Valley Creek (VCGU), Big Boulder Creek (BBG) and Morgan Creek above West Fork Morgan Creek (MCabvWFMC). Long-term streamflow information is lacking in the upper Salmon River Basin, especially for basins smaller than 20 to 30 mi2. Additional streamflow data collected in these smaller basins not only would provide much needed information, but also could improve the accuracy of regression equations used to estimate streamflows at ungaged sites.
Continuous summer water temperatures were recorded at BBG, BB1, CH4, BE1, CH3, ML1, CH2, CH1, Morgan Creek above Alder Creek (MCabvAC), MCabvWFMC, and MC1. Permission to access private property precluded installation of data loggers above diversions on Bear and Mill Creeks.
Big Boulder Creek is an easterly flowing stream in the central part of the upper Salmon River Basin. Big Boulder Creek is a tributary to the East Fork Salmon River and its headwaters originate in the White Cloud Peaks (fig. 1). The Big Boulder Creek basin covers 26.9 mi2, of which about 41 percent is forest. Mean elevation in the basin is about 8,810 ft above sea level and the basin receives an average of 29.1 in/yr of precipitation.
A short-term streamflow-gaging station (Big Boulder Creek near Clayton; 13297500; BBG) was installed on Big Boulder Creek about 0.75 mi upstream of the confluence with the East Fork Salmon River and operated from April 1 through October 3, 2005. The USGS also operated a long-term streamflow-gaging station at this location from May 1926 through January 1930. This gaging station is upstream of the two active diversions on Big Boulder Creek (fig. 4). A plot of the continuous daily mean discharge at BBG during WY05 is presented in figure 5, along with markers indicating when field data were collected at study site BB1, between the mouth and the first upstream diversion.
Additional analyses were completed to relate streamflows in Big Boulder Creek during WY05 to long-term streamflows. The July, August, and September daily mean discharge hydrograph at BBG for WY05 and the 80-, 50-, and 20-percent monthly exceedance statistics for the period of record (1926-29 and 2005) are presented in figure 6. The plot shows that WY05 streamflows in Big Boulder Creek generally were near or slightly below the long-term median (50-percent exceedance) during the months shown. Analyses of WY05 and long-term monthly exceedance discharge data for Big Boulder Creek are presented in table 2. The July, August, and September 80-percent exceedances for WY05 were slightly above the long-term values, although the 20-percent exceedances were all below the long-term values. Table 2 also shows the 80-, 50-, and 20-percent monthly exceedance discharge estimates and confidence limits based on regional regression equations (Hortness and Berenbrock, 2001). Comparison between long-term statistic values and values calculated on the basis of the regression equations can provide some insight as to the applicability of the regression equations for Big Boulder Creek. In this case, the regression estimates tend to be lower than the long-term values, indicating that the equations, to some degree, could underestimate streamflow conditions in Big Boulder Creek.
The lower Big Boulder Creek (BB1) discharges required for maximum WUA ranged from 24 to 39 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 3). Discharge required for maximum WUA was 24 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 18 to 27 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 15 to 27 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 1, 4, and 6 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). Appendix A provides more information summarizing these study results.
Summer (July through September) discharges for BB1 were estimated on the basis of regression equations and are listed in table 3. Median discharge (Q.50) estimates were 32.1 ft3/s for July, 15.1 ft3/s for August, and 10.7 ft3/s for September. The mean annual discharge estimate was 15.2 ft3/s.
Temperature recording data loggers were deployed at BBG and BB1 in early June 2005 (fig. 7). Data loggers were retrieved in mid-September 2005. After downloading and reviewing the data, June 12 through September 12 (93 days) was selected as the period of record for calculating stream temperature metrics.
Analysis of the stream temperature records for Big Boulder Creek indicated a slight warming trend downstream of BBG to BB1 (fig. 7). However, the difference in temperature between BBG and BB1 was only slightly greater than the measurement error associated with the temperature recording data logger (± 0.4). The difference in MDMT between BBG and BB1 on any given day was less than 0.5ºC, 97 percent (3 of 93 days) of the time.
Individual metric calculation results showed the MDMT was 16.2ºC at BBG and 16.6ºC at BB1, well below the MDMT threshold of 21.0ºC that, according to Poole and others (2001), can create a thermal barrier that would block adult Chinook salmon from migrating to their spawning grounds. The MDMT at both sites also was below the 18.0ºC threshold that may block bull trout migration (J. Dunham, U.S. Forest Service, written commun., 2004).
The MDAT was 13.5ºC at BBG and 14.0ºC at BB1, well below the 17.8ºC MDAT upper temperature threshold that according to McHugh and others (2004) can decrease the survival rate of summer Chinook salmon juveniles in natal streams.
Comparing the temperature regime at the two sites on Big Boulder Creek to the IDEQ criteria for protection of coldwater biota (applicable from June 22 through September 21) indicates the temperature regime at BBG and BB1 was below the 19.0ºC MDAT and 22.0ºC MDMT criteria. A summary of individual temperature metrics for all study sites can be accessed at http://id.water.usgs.gov/projects/salmon_streamflow.
Challis Creek is an easterly flowing tributary to the Salmon River with its mouth just north of Challis, Idaho. The Challis Creek headwaters are along the northern-most boundary of the upper Salmon River Basin (fig. 1). The Challis Creek Basin covers about 148 mi2, of which about 49 percent is forested. Mean elevation in the basin is about 7,450 ft above sea level and the basin receives an average of 23.1 in/yr of precipitation. Six study sites were in the Challis Creek Basin. Four of those sites were on the main stem of Challis Creek (CH1, CH2, CH3, and CH4) and the other two sites were on Bear Creek (BE1) and Mill Creek (ML1), both major tributaries of Challis Creek (fig. 8).
No continuous record streamflow data were collected on Challis Creek during WY05. Historical continuous record streamflow data are available for locations on Challis Creek about 6.9 (Challis Creek near Challis; 13299000) and 4.9 mi (Challis Creek below Jeffs Creek, near Challis; 13299200) upstream of the mouth for water years 1944-63 and 1963-70, respectively. The 80-, 50-, and 20-percent monthly exceedance discharge values for those gaging stations for the periods of record along with exceedance estimates derived from regional regression equations (Hortness and Berenbrock, 2001) are presented in tables 4 and 5. These values indicate that the regression equations generally may tend to underestimate monthly streamflow statistics in the Challis Creek Basin. In addition to historical data, instantaneous discharge measurements were made at all study sites during water WY05 and are presented in table 6. Because of their proximity, the similarities in size, and other basin characteristics of the Challis and Morgan Creek basins, it also may be possible to make some inferences as to the characteristics of streamflow in Challis Creek based on information from Morgan Creek.
Upper Challis Creek (CH4) discharges required for maximum WUA ranged from 22 to 37 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 7). Discharge required for maximum WUA was 16 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 16 to 22 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 10 to 19 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 3, 4, and 5 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). Appendix B provides more information summarizing these study results.
Summer (July through September) discharges for CH4 were estimated on the basis of regression equations and are listed in table 7. Median discharge (Q.50) estimates were 17.3 ft3/s for July, 8.7 ft3/s for August, and 6.9 ft3/s for September. The mean annual discharge estimate was 17.4 ft3/s.
Lower Bear Creek (BE1) discharges required for maximum WUA ranged from 8 to 26 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 7). Discharge required for maximum WUA was 11 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 5 to 14 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 4 to 14 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 3, 5, and 6 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). Appendix C provides more information summarizing these study results.
Summer (July through September) discharges for BE1 were estimated on the basis of regression equations and are listed in table 7. Median discharge (Q.50) estimates were 10.1 ft3/s for July, 5.1 ft3/s for August, and 3.8 ft3/s for September. The mean annual discharge estimate was 8.9 ft3/s.
Upper middle Challis Creek (CH3) discharges required for maximum WUA ranged from 19 to 67 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 7). Discharge required for maximum WUA was 27 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from <11 to 23 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and <11 to 11 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 1, 5, and 6 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). In some cases, the passage criteria were less than the lower limit of the model conditions. In those cases graphs for a given transect may be useful to estimate the discharge required for passage. Appendix D provides more information summarizing these study results.
Summer (July through September) discharges for CH3 were estimated on the basis of regression equations and are listed in table 7. Median discharge (Q.50) estimates were 47.8 ft3/s for July, 24.0 ft3/s for August, and 19.9 ft3/s for September. The mean annual discharge estimate was 46.6 ft3/s.
Lower Mill Creek (ML1) discharges required for maximum WUA ranged from 9 to 18 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 7). Discharge required for maximum WUA was 9 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 6 to 9 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 3 to 9 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 3, 5, and 6 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). Appendix E provides more information summarizing these study results.
Summer (July through September) discharges for ML1 were estimated on the basis of regression equations and are listed in table 7. Median discharge (Q.50) estimates were 11.7 ft3/s for July, 6.0 ft3/s for August, and 4.9 ft3/s for September. The mean annual discharge estimate was 15.4 ft3/s.
Lower middle Challis Creek (CH2) discharges required for maximum WUA ranged from 26 to 50 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 7). Discharge required for maximum WUA was 22 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from <6 to 18 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and <6 to 14 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 1, 6, and 7 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). In some cases, the passage criteria were less than the lower limit of the model conditions. In those cases, graphs for a given transect may be useful to estimate the discharge required for passage. Appendix F provides more information summarizing these study results.
Summer (July through September) discharges for CH2 were estimated on the basis of regression equations and are listed in table 7. Median discharge (Q.50) estimates were 59.6 ft3/s for July, 29.9 ft3/s for August, and 25.5 ft3/s for September. The mean annual discharge estimate was 64.5 ft3/s.
Lower Challis Creek (CH1) discharges required for maximum WUA ranged from 15 to 55 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 7). Discharge required for maximum WUA was 35 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 15 to 19 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 7 to 11 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 5, 6, and 7 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). Appendix G provides more information summarizing these study results.
Summer (July through September) discharges for CH1 were estimated on the basis of regression equations and are listed in table 7. Median discharge (Q.50) estimates were 59.2 ft3/s for July, 29.8 ft3/s for August, and 26.1 ft3/s for September. The mean annual discharge estimate was 74.1 ft3/s.
Temperature recording data loggers were deployed at four locations in Challis Creek (CH4, CH3, CH2, and CH1), and two major tributaries Bear Creek (BE1) and Mill Creek (ML1) in 2005 (fig. 8). All data loggers were deployed in June 2005. All data loggers were retrieved in mid-September 2005. After downloading and reviewing the data, June 12 through September 12 (93 days) was selected as the period of record for calculating stream temperature metrics.
Analysis of the stream temperature records for Challis Creek indicated a slight cooling trend downstream of CH4 to CH2 and then a pronounced warming trend downstream of CH2 to CH1 (fig. 9). This warming trend appears to strengthen over time and most likely is due to increasing air temperatures and the diversion of streamflow for irrigation over the course of the summer.
Individual metric calculation results showed the MDAT was 16.2ºC at CH4, 15.3ºC at CH3, 16.6ºC at CH2, and 19.5ºC at CH1. The MDAT at CH4, CH3, and CH2 was below the 17.8ºC MDAT upper temperature threshold that according to McHugh and others (2004) can decrease the survival rate of summer Chinook salmon juveniles in natal streams; however, the MDAT at CH1 was above the 17.8ºC MDAT upper temperature threshold.
The MDMT was 21.0ºC at CH4, 20.2ºC at CH3, 20.8ºC at CH2 and 26.3ºC at CH1. The MDMT at all sites was very near or above the MDMT threshold of 21.0ºC that, according to Poole and others (2001), can create a thermal barrier that would block adult Chinook salmon from migrating to their spawning grounds. The MDMT at all sites exceeded the 18.0ºC threshold that may block bull trout migration (J. Dunham, U.S. Forest Service, written commun., 2004).
The temperature regime at all sites except CH1 was below the 19.0ºC MDAT and below the 22.0ºC MDMT IDEQ criteria, for protection of coldwater biota (applicable from June 22 through September 21). A summary of individual temperature metrics for all study sites can be accessed at http://id.water.usgs.gov/projects/salmon_streamflow.
A temperature recording data logger was deployed at BE1 downstream of the diversions in early June 2004 (fig. 10). The data logger was retrieved in late September 2004. After downloading and reviewing the data, June 12 through September 12 (93 days) was selected as the period of record for calculating stream temperature metrics.
Individual metric calculation results showed that the MDAT was 11.4ºC at BE1, well below the 17.8ºC MDAT upper temperature threshold that according to McHugh and others (2004) can decrease the survival rate of summer Chinook salmon juveniles in natal streams.
The MDMT was 14.4ºC at BE1, well below the 18.0ºC threshold that may limit bull trout habitat and block passage because of high water temperatures (J. Dunham, U.S. Forest Service, written commun., 2004). The MDMT also was below the 21.0ºC threshold that, according to Poole and others (2001), can create a thermal barrier that can possibly block adult Chinook salmon from migrating to their spawning grounds.
The temperature regime at BE1 also was below the 19.0ºC MDAT and 22.0ºC MDMT IDEQ criteria for the protection of coldwater biota (applicable June 22 through September 21). A summary of individual temperature metrics for all study sites can be accessed at http://id.water.usgs.gov/projects/salmon_streamflow.
A temperature recording data logger was deployed at ML1 downstream of all diversions in early June 2004 (fig. 11). The data logger was retrieved in late September 2004. After downloading and reviewing the data, June 12 through September 12 (93 days) was selected as the period of record for calculating stream temperature metrics.
Individual metric calculation results showed that the MDAT was 18.1ºC at ML1, slightly above the 17.8ºC MDAT upper temperature threshold that according to McHugh and others (2004) can decrease the survival rate of summer Chinook salmon juveniles in natal streams.
The MDMT was 22.0ºC at ML1, above the 18.0ºC threshold that may limit bull trout habitat and block passage because of high water temperatures (J. Dunham, U.S. Forest Service, written commun., 2004). The MDMT at ML1 also was above the 21.0ºC threshold that according to Poole and others (2001) can create a thermal barrier that can possibly block adult Chinook salmon from migrating to their spawning grounds.
Comparison of the temperature regime at ML1 to the IDEQ criteria of 19.0ºC MDAT and 22.0ºC MDMT for the protection of coldwater biota (applicable from June 22 through September 21), indicates that the MDAT was below the 19.0ºC criterion, although the MDMT was at the 22.0ºC MDMT criterion. A summary of individual temperature metrics for all study sites can be accessed at http://id.water.usgs.gov/projects/salmon_streamflow.
Morgan Creek is an easterly flowing tributary to the Salmon River with its mouth just north of Challis, Idaho. The Morgan Creek headwaters are along the northern-most boundary of the upper Salmon River Basin (fig. 1). The Morgan Creek Basin covers about 107 mi2, of which about 36 percent is forested. Mean elevation of the basin is about 7,140 ft above sea level and the basin receives an average of 20.1 in/yr of precipitation. One study site (MC1) was on Morgan Creek about 0.5 mi upstream of the mouth (fig. 12).
The USGS began operating a continuous-record streamflow-gaging station on Morgan Creek (Morgan Creek above West Fork Morgan Creek; 13299255; MCabvWFMC) on March 30, 2005, for the U.S. Forest Service. This gaging station is on the main stem of Morgan Creek just upstream of West Fork Morgan Creek and about 6 mi upstream of the mouth. Active streamflow diversions are upstream and downstream of the gaging station and do affect the streamflow at the gaging station. A plot of the continuous daily mean discharge in Morgan Creek for WY05 is presented in figure 13, along with markers indicating the times when field data were collected at the study site (MC1).
Additional analyses were completed that compared streamflows in Morgan Creek to estimates of long-term streamflow statistics. The July, August, and September daily mean discharge hydrograph for MCabvWFMC for WY05 along with the estimated 80-, 50-, and 20-percent monthly exceedances based on regression equations developed by Hortness and Berenbrock (2001) are presented in figure 14. Monthly exceedance statistics for July, August, and September streamflows at MCabvWFMC during WY05 along with the estimated monthly exceedances and their confidence limits (Hortness and Berenbrock, 2001) are presented in table 8. Daily mean discharges for MCabvWFMC are affected by upstream diversions; however, monthly exceedance estimates are indicators of natural streamflow conditions unaffected by diversions. The effects of diversions on streamflow at MCabvWFMC are quite apparent in figure 14, when compared to estimates of long-term monthly statistics.
The lower Morgan Creek (MC1) discharges required for maximum WUA ranged from 15 to 42 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout (table 9). The very low WUA for bull trout spawning shown in appendix figure H2 is attributed to the lack of suitable substrate. Discharge required for maximum WUA was 30 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from <11 to 15 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and <11 ft3/s greater than 10 percent of the contiguous channel width, respectively (see transects 2, 3, and 4 photographs at http://id.water.usgs.gov/projects/salmon_streamflow). In some cases, the passage criteria were less than the lower limit of the model conditions. In those cases, graphs for a given transect may be useful to estimate the discharge required for passage. Appendix H provides more information summarizing these study results.
Summer (July through September) discharges for MC1 were estimated on the basis of regression equations and are listed in table 9. Median discharge (Q.50) estimates were 31.2 ft3/s for July, 16.4 ft3/s for August, and 14.9 ft3/s for September. The mean annual discharge estimate was 55.5 ft3/ s.
Temperature recording data loggers were deployed at three locations in Morgan Creek in 2005 (fig. 15). These locations included MCabvAC, MCabvWFMC, and MC1. All data loggers were deployed in June 2005. All data loggers were retrieved in mid-September 2005. After downloading and reviewing the data, June 12 through September 12 (93 days) was selected as the period of record for calculating stream temperature metrics.
Analysis of the stream temperature records for Morgan Creek indicated a pronounced warming trend downstream of MCabvAC to MC1 (fig. 15). This warming trend appears to strengthen over time and most likely is due to increasing air temperatures and the diversion of streamflow for irrigation over the course of the summer.
Individual metric calculation results showed the MDAT was 14.8ºC at MCabvAC, 18.6ºC at MCabvWFMC, and 19.0ºC at MC1. The MDAT at MCabvAC was below, while the MDAT at MCabvWFMC and MC1 was above the 17.8ºC MDAT upper temperature threshold that according to McHugh and others (2004) can decrease the survival rate of summer Chinook salmon juveniles in natal streams.
The MDMT was 19.0ºC at MCabvAC, 22.2ºC at MCabvWFMC, and 24.1ºC at MC1. The MDMT at MCabvAC was below, while the MDMT at MCabvWFMC and MC1 was above the MDMT threshold of 21.0ºC that according to Poole and others (2001) can create a thermal barrier that would block adult Chinook salmon from migrating to their spawning grounds. The MDMT at all sites exceeded the 18.0ºC threshold that may block bull trout migration (J. Dunham, U.S. Forest Service, written commun., 2004).
The temperature regime at MCabvAC was below the 19.0ºC MDAT and the 22.0ºC MDMT IDEQ criteria, for protection of coldwater biota (applicable from June 22 through September 21). The temperature regime at MCabvWFMC was below the 19.0ºC MDAT, but above the 22.0ºC MDMT criteria. The temperature regime at MC1 was above the 19.0ºC MDAT and the 22.0ºC MDMT criteria. A summary of individual temperature metrics for all study sites can be accessed at http://id.water.usgs.gov/projects/salmon_streamflow.
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