ScholarWorks at University of Montana

Whirling disease, caused by the myxozoan parasite Myxobolus cerebralis, remains a serious health threat to salmonid fish in the western U.S. Although various aspects of this host-parasite system have been studied, investigations examining the overall epizootiology of whirling disease in an ecosystem are lacking. Therefore, in June 1998, such a study was initiated in the Rock Creek watershed of west central Montana. Parameters examined included assessing the intensity of infection in trout using sentinel cages stationed throughout the drainage and determining the percentage of Tubifex tubifex releasing M. cerebralis at sentinel cage and other localities. Also, habitat and water quality parameters were measured. Overall, the intensity of M. cerebralis infections in sentinel trout increased significantly throughout the drainage between June of 1998 and 2006 with the biggest jump occurring between 1998 and 1999. In addition, the range of M. cerebralis expanded considerably over this period. There was no strict correlation between habitat condition and the occurrence of the parasite as fish became heavily infected in optimal and marginal habitats. During this period, the parasite apparently caused a dramatic decline in wild rainbow trout densities but the brown trout population numbers increased. However, it now appears that disease intensity peaked in 2006 and is on the decline in this watershed. The decline cannot be directly attributed to a change in the prevalence of M. cerebralis-infected T. tubifex as these numbers remained statistically the same from 1998 to 2008. Similarly, changes in water temperature and water flow do not account for the decrease in disease intensity. However, it is possible that wild rainbow trout are developing some resistance to the parasite, a phenomenon recently documented to be occurring in the Willow Creek Reservoir of southwest Montana.

The State of Montana assessed injuries to natural resources resulting from the actions of ARCO and its predecessors in the 1980s and 1990s. In the final report summarizing injuries, the Northern river otter (Lontra canadensis) was identified as one species greatly impacted by habitat degradation. Recent research by Montana Fish, Wildlife & Parks and MFWP trapping records demonstrate that otters have begun to return to the UCFRB, but this population appears markedly less robust than those in other drainages in north - and southwestern Montana. Working cooperatively with MFWP, we are conducting a detailed study documenting the status and distribution of otters in the UCFRB. Surveys of the Clark Fork river drainage from Silver Bow Creek to the Warm Springs Ponds and downriver to Bonner including main tributaries are being conducted. Otter and beaver sign are being catalogued, DNA analyses of otter hair and fecal samples are being performed to identify individuals, and an assessment of current habitat conditions necessary to support otters is being made.

Preliminary results from the summer of 2009 catalogued 13 latrine sites and 6 possible den sites along the Clark Fork River. Forty-nine scats were collected from which a subsample will be analyzed for DNA. Fifty-eight beaver lodges and 8 dams were observed along the Clark Fork River proper, 6 lodges were observed along the Little Blackfoot River and abundant evidence of beaver activity was observed when walking Silver Bow Creek. This research will continue through 2011.

Current environmental conditions in Georgetown Lake are being quantified to examine long term trends and to provide a baseline for future reference. Preliminary findings on nutrients, dissolved oxygen, macrophyte coverage, phytoplankton composition and abundance, and water clarity will be presented. Analysis of historic dissolved oxygen data collected by Montana Fish Wildlife and Parks indicates that late winter oxygen concentrations reach low levels and are decreasing through time.

The 2008 removal of Milltown Dam on the Clark Fork, near Bonner was predicted to affect pier and abutment foundations of nearby bridges. The substantial contraction of streamflow at the bridge exerted hydraulic forces on these structures not experienced when they were in the backwater of Milltown Reservoir. Countermeasures used to mitigate predicted scour and erosion included substantial modification of piers and abutments of the I-90 bridges that cross the Blackfoot River near the confluence with the Clark Fork. With Milltown Dam removed and scour countermeasures completed, the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, began monitoring hydraulic and scour conditions at the I-90 bridges beginning with the spring 2009 runoff season. The purposes of the multi-year monitoring effort are to measure the effects of high-flow conditions on the I-90 bridge piers and abutments and nearby stream channel morphology, to compare measured hydraulic and scour data to scour and erosion predictions from earlier models, to characterize the extent to which scour and erosion effects are due to local hydraulic factors versus more broad-based geomorphic factors, and to provide stream-velocity data for this reach to aid in evaluating the possibility of bull trout passage. Real-time hydroacoustic instrumentation was installed at bridge piers, bathymetry of the streambed was surveyed before and after runoff, and topography of the riprap blanket at bridge abutments and cross sections near bridges also were surveyed. Finally, hydraulic data including water stage and slope and flow velocity were collected.

About 6.6 million cubic yards of sediments enriched in trace elements from historical mining operations were deposited in Milltown Reservoir after construction of Milltown Dam in 1907. Milltown Dam was removed in March 2008, as part of remedial activities. In preparation for the removal of Milltown Dam, permanent drawdown of Milltown Reservoir began in June 2006.

The annual mass balance (that is, the inflow load minus the outflow load) of suspended sediment and trace element loads within the project area (the historical Clark Fork channel and floodplain affected by impoundment of water behind Milltown Dam) were estimated for water years 2004–2009. During water years 2004–2005, inflow loads of suspended sediment and most trace elements exceeded outflow loads indicating net gain in the project area. Net loss of suspended sediment and trace elements from the project area began after the start of the permanent drawdown in June 2006 and continued through water year 2009. In water year 2008, there was net loss of about 391,000 tons of suspended sediment and about 157 tons of unfiltered-recoverable copper with most of the transport occurring after the removal of Milltown Dam in March. Substantially smaller net loss of suspended sediment and copper occurred during water year 2009 (provisional estimates of about 76,000 and 31 tons, respectively) than during water year 2008 even though streamflow conditions were similar. The estimated cumulative net loss of suspended sediment from the project area from June 2006 through water year 2009 is about 623,000 tons.

The 2008 breaching of Milltown Dam resulted in base-level lowering of 9 m at the dam site and introduced a pulse of fine reservoir sediment into the gravel and cobble-bedded Clark Fork River. Studies of the geomorphic effects of the dam removal have evaluated the volume of material eroded from the Blackfoot and Clark Fork arms of Milltown reservoir, downstream transport and deposition of that sediment, and resulting changes in channel morphology. These efforts have incorporated bedload and bed-material sampling, surveys of topographic change, and aerial photograph analysis. In the first two years following dam breaching, successive peak flows with similar magnitudes (3-year recurrence interval) eroded several hundred thousand cubic meters of sediment from Milltown reservoir. Reservoir erosion and downstream geomorphic adjustments were far greater in the first year following removal, when readily mobilizable fines were eroded and transported downstream, than in the second year. Downstream topographic changes (e.g., aggradation) have been limited in study reaches within 4 km of the dam site, but more significant sediment accumulation has been observed in the multi-thread reach extending between the Reserve Street bridge in Missoula and the Bitterroot River confluence (from 21 to 25 km downstream of the dam site). Substantial infiltration of fine reservoir sediments into the interstices of the gravel and cobble bed has also been observed. Studies are ongoing to assess the duration and spatial extent of geomorphic changes resulting from the dam removal.