Welcome to FishSalmonRiver.com
Your complete source for information on fishing the Salmon River, NY and Eastern Lake Ontario regions
NYSDEC LAKE ONTARIO ANNUAL REPORT 1999


Comparison of Pre- and Post-Baseflow Fish Communities
and Natural Reproduction of Chinook Salmon in
Salmon River, 1999

by

D. L. Bishop
New York State Department of Environmental Conservation
Cortland, NY 13045


J. H. Johnson
U.S. Geological Survey, Tunison Laboratory of Aquatic Sciences
Cortland, NY 13045





Introduction Figure 1  Map of sites
Methods Table 1   Daily min mean and max of water Temps
        Temperature Table 2   Correlation Coefficients
        Fish Community Table 3   of species captured in Salmon River
        Electrofishing Table 4  Numbers of each species captured in Salmon River
Results and Discussion Table 5   Pairwise t-tests
        Temperature  
        Fish Community  
Conclusion  
References  





Introduction


Seasonal baseflows mandated by the Federal Energy Regulatory Commission hydroelectric licensing agreement (FERC 1996) have resulted in a dramatic increase in natural reproduction of chinook salmon in the Salmon River. Substantial, but undocumented natural reproduction occurred in 1997 but severe flooding in the winter of 1997-1998 is believed to have curtailed production in 1998. While no pre-baseflow survey data exists, anecdotal observations by NYSDEC personnel suggest that little natural reproduction of chinook salmon occurred prior to the baseflows (Les Wedge, pers. comm.).

The hydroelectric project was formerly run as a peaking operation which resulted in alternating periods of generation flows (750-2000 cfs) and leakage (20 cfs). This resulted in frequent de-watering of the majority of the river bed. The current mode of operation provides seasonal baseflows, which have been in effect since fall, 1996. The baseflows are 335 cfs September-December, 285 cfs January-April and 185 cfs May-August.

Occasional deviations from the baseflows are caused by water shortages, surpluses, and scheduled white-water events in the summer. Drought conditions in fall, 1998, for example, resulted in a reduction of baseflow to 185 cfs for November. At no time, however, is the river bed de-watered as in the past.

This report documents post-baseflow summer temperatures and natural reproduction of chinook salmon. A general description of the fish community for pre- and post- baseflow time periods is also provided.




Methods


Temperature
Waddle (1989) provided an analysis of pre-base flow temperatures in the river. The analyses focused on determining the magnitude of temperature effects due to power plant operation and air temperature, and to develop predictions of water temperatures under various flow conditions.

Post-base flow temperature data were collected in 1997, 1998 and 1999. StowAway XTI temperature loggers manufactured by the Onset Computer Corporation (Pocasset, MA) were deployed at various sites on the Salmon River to measure summer river temperatures. Summer air temperature data collected by the National Weather Service at Hancock Airport in Syracuse were downloaded from the Internet (Click here to go there) for June, July and August of 1997, 1998 and 1999. Pearson correlation coefficients were computed for each year and site to study the effects of air temperature on water temperature.

Fish Community

Chinook salmon seining
An index seining program was initiated in 1999 by USGS and NYSDEC to gain information on the spatial and temporal size and distribution of wild chinook in the river. Sixteen (16) seine hauls were made at 4 different sites from 19 May to 24 June. The seine was a 6.1 m (20') bag seine 1.8 m (6') deep with 0.3 cm (1/8") mesh. Hauls were made by stretching the seine perpendicular to the current and sweeping downstream toward one bank to a suitable landing area. A sample consisted of one seine haul per site. Obstacles on the river bottom and differences in the lengths of the hauls prevented direct comparison of catches per unit of effort but do provide a rough estimate of density considering the range of numbers captured between sites and dates. A map of all sampling sites is provided in Figure 1.

All species captured were counted and a sample of chinook were measured (total length) for each haul. Mean lengths of chinook captured for each date and site were compared using a pairwise t-test multiple comparison procedure (SAS Proc GLM, SAS Institute 1987).

Electrofishing

Data from two NYSDEC electrofishing surveys are used in this analysis. One survey was carried out in 1980 (pre-base flow) and the other was in 1999 (post-base flow). The higher flows in 1999 and low conductivity (60-67 µmohs) presented difficulty in the electrofishing efforts. The survey was designed to collect samples that were representative of the species present and their relative abundances.

The 1999 survey was done from 10 August to 12 August. Nine sites were sampled. Riffle and run habitat were sampled at all sites with a canoe mounted 3000 watt Pincor generator connected to a NYSDEC "gray box" converter (220 DC volts, unknown amps). One crew member towed the canoe and controlled the cords. Two crew members operated the anodes which were connected to a splitter with 25' leads and 3 scappers collected fish.

Pool habitat was sampled at the Papermill Pool and the pool just below the Staircase with a Smith-Root model SR12 electrofishing boat. Voltage was set to "high range" DC, 60 pulses per second (pps) and percent of range was set at 100% which resulted in approximately 6 amps. The pools were generally sampled by repeatedly working up to the tops and applying power as the boat drifted downstream.

The 1980 survey consisted of sampling 5 sites from 4 August to 15 August. This survey was designed to estimate populations of salmonids by reduction on subsequent runs. The sites sampled were limited to the upper portion of the river (above Rt. 81) and 3 of the sites were located directly below tributaries known to produce wild salmonoids; Beaverdam Brook, Trout Brook and Orwell Brook. In contrast to the 1999 electrofishing survey, low flows present in 1980 allowed both pool and riffle habitat to be sampled at each site. A 3500 watt bank mounted generator was used.




Results and Discussion

Temperature
Waddle (1989) concluded that changes in air temperature had a greater influence on river temperatures than the amount of water being released from Lighthouse Hill Reservoir, with the effect greater in more downstream sections. He attributed this to the fairly constant and relatively warm temperature (near equilibrium) of the water being released which, in turn, limits the ability of the released water to influence (cool) downstream temperatures.

Our analyses strongly support the conclusions drawn by Waddle (1989). Monthly means of daily highs, lows, and averages of river and air temperatures for July and August of 1997, 1998 and 1999 are presented in Table 1. Sites in the upper reaches generally remained around 22 C all the time during July and August. Sites in the lower reaches were more affected by air temperature, showing larger diurnal temperature fluctuations and more variability in the daily highs, lows and averages.

Pearson correlations show the effects of air temperature on river temperature and the increasing influence in the more downstream sites (Table 2). Daily highs and lows occurred latest, 1600-1800 hrs and 0800 hrs, respectively, in the lowest section (Douglaston). In more upstream sites, daily highs, which were lower than those in the downstream sites were typically reached earlier in the day (1400-1600 hrs at Salmon River Hatchery) and daily lows, which were higher than those in downstream sites were reached much earlier (2200 hrs at Salmon River Hatchery). Night-time temperatures remained stable at the daily low in the upstream sites until the water began warming again around 0800 hrs.

Fish Community
Post-base flow fish community surveys showed that the river is capable of producing large numbers of wild chinook salmon under the current baseflow regime but is limited, particularly in the lower reaches, for producing or supporting other juvenile salmonids during the summer. Substantial numbers of lake run adult Skamania steelhead, landlocked Atlantic salmon, and brown trout, however, have been observed in pools in the upper river during summer months of recent years. Our fisheries surveys were primarily focused on juvenile salmonid habitat in riffle/run areas and do not reflect the presence of these large fish. Species captured in all surveys are presented in Table 3. Total numbers of each species caught at each site in the 1999 surveys are provided in Table 4.

The 1999 chinook salmon seining survey showed that the young-of-year (YOY) chinook salmon were relatively abundant in the river when the survey began in late May and that most had left by late June when the survey concluded. The multiple range pairwise t-tests comparing mean lengths of chinook and numbers caught for the different sites and dates demonstrate the decreasing density and increasing size of YOY chinook through time (Table 5).

Chinook tended to smolt and emigrate to the lake by the time they reached a total length of approximately 70 mm. They were relatively abundant and averaged 40.4 mm and 45.6 mm total length on 19 May at Pineville and Altmar, respectively. The largest catch of chinook came on 25 May when 279 were captured at Douglaston and the average size was 56.7 mm. Mean sizes increased through time reaching 60-65 mm by 24 June when density had decreased dramatically. Relatively high numbers of juvenile chinook were captured at each of the sites surveyed on one or more dates demonstrating the importance of the entire river for spawning and nursery habitat.

The 1999 DEC electrofishing survey suggested that very few juvenile salmonids were in the river during August of 1999. Only one wild young-of- year steelhead was captured and that was in the Upper Fly section directly below the tail race. Fourteen (14) YOY Atlantic salmon were also captured at this site and one more was captured at the next site downstream adjacent to Salmon River Hatchery. These fish were from a SUNY College of Environmental Science and Forestry (ESF) experimental stocking of 102,000 fry stocked at various sites between the tail race and CO. RT. 2A. Electrofishing surveys carried out independently by SUNY ESF personnel at the stocking sites revealed sporadic survival among sites including some survival at CO. RT. 2A (Steve Coghlan, SUNY ESF graduate student, pers. comm.).

The most commonly captured species was fantail darter, which was abundant on the entire river. Fallfish were also captured at every site. Relatively high numbers of cutlips minnows were captured in the upper reaches and longnose dace were relatively abundant in the lower reaches. Northern hog suckers appeared to be limited to the deeper pools which were only surveyed at the Papermill and the Staircase. White suckers were only captured at the Papermill pool.

Species compositions were very similar for the pre- and post-baseflow time periods but a few interesting differences are apparent. The 1980 survey showed that there were substantial numbers of American eel in the river. The lack of American eel in the 1999 surveys was probably due to the precipitous decline of yellow eels entering the St. Lawrence/Lake Ontario system since the mid-1980s (Casselman et. al 1997) rather than a reflection of a reduction of suitable habitat in the river since base flows were initiated. The presence of hatchery brown trout yearlings in the 1980 sample was a reflection of a stocking policy that was in place at the time. More young of year wild steelhead and hatchery yearling steelhead were captured in the 1980 survey. This was probably a reflection of station location because 1980 stations were purposely located below tributaries that were colder than the main river and known to produce wild salmonines. While YOY smallmouth bass were captured in both years, the increased volume of the river and associated increases in all habitat types in 1999 suggest that natural production of smallmouth bass may have increased since the initiation of base flows.




Conclusions

Seasonal base flows initiated in the mid-1990s resulted in a dramatic, though highly variable, increase in production of wild chinook salmon in the Salmon River. Environmental conditions probably made 1999 a worst case scenario for production of wild steelhead in the river. The extreme heat and a 10,000 cfs flood event in July probably caused conditions in the river to be less conducive to juvenile steelhead survival than average.

Elevated summer temperatures, particularly in 1999, appear limiting to juvenile salmonines which require year-round residence (i.e. steelhead, coho salmon and brown trout) with the possible exception of Atlantic salmon. Failure to catch wild yearling steelhead in the chinook seining program and the extreme low abundance of wild YOY steelhead encountered in August electrofishing efforts suggest that the potential for wild steelhead production from the main stem of the river is probably low. The fact that some of the Atlantic salmon stocked in the spring as fry survived the extreme heat and the flood of 1999 suggest that the river may offer a unique opportunity for rearing Atlantic salmon juveniles in the relative absence of juvenile steelhead or other salmonine competitors requiring year-round residence.




References

Casselman, J.M., L.A. Marcogliese, and P.V. Hodson 1997. Recruitment index for the upper St. Lawrence River and Lake Ontario eel stock: A re-examination of eel passage at the R.H. Saunders Hydroelectric Generating Station at Cornwall, Ontario, 1974-1995. In Peterson, R.H. (Editor). 1997 The American eel in eastern Canada: stock status and management strategies. Proceedings of Eel Management Workshop. January 13-14, 1997. Quebec City, QC. Can Tech. Rep. Fish. Aquat. Sci. 2196: v+174p.

Federal Energy Regulatory Commission (FERC). 1996. Order issuing original license (Major Project). Washington, DC: Federal Energy Regulatory Commission. FERC Project No. 11408, New York.

SAS Institute Inc., 1987. SAS/STAT guide for personal computers, Version 6. Cary NC. 1029 pp.

Waddle, T.J. 1989. Water temperature data analysis and simulation for the Salmon River, Oswego County, New York, Summer, 1986. U.S. Fish and Wildl. Serv. National Ecology Research Center, Fort Collins, CO. 83pp.



Figure 1.

Salmon River sampling sites


Figure One





Table 1.

Daily minimum, mean, and maximum water temperatures (°C) and coefficients of variation for Salmon River sampling sites and Syracuse air temperatures

August
July
MIN Mean Max Min Mean Max
SITE YEAR MEAN CV MEAN CV MEAN CV MEAN CV MEAN CV MEAN CV
DOUGLASTON 1999 21.6 5.7 23.6 5.3 26.0 6.2 20.0 6.7 21.8 5.5 23.8 6.0
BELOW 81 1997 18.7 9.2 21.3 7.7 24.2 7.5 19.0 6.9 21.2 5.9 23.7 6.9
CO RT 2A 1997 18.2 7.5 20.7 6.7 23.4 7.3 18.8 6.5 20.9 5.4 23.0 6.4
  1999 20.8 4.8 23.0 4.1 25.6 6.4 19.6 5.5 21.7 4.2 24.1 5.8
TRESTLE 1998 20.1 4.2 21.1 4.9 22.6 7.1 21.4 3.0 22.5 3.1 24.3 6.6
  1999 21.4 3.5 22.5 2.4 24.1 4.0 20.9 2.5 21.9 2.0 23.6 3.3
HATCHERY

1997 19.8 3.4 20.3 3.4 21.1 3.7 21.0 2.5 21.4 2.9 22.1 4.0
  1998 20.7 4.6 21.2 4.9 21.8 5.9 22.2 1.4 22.8 2.7 23.8 8.0
  1999 21.9 2.8 22.3 2.1 23.1 2.2 21.8 1.8 22.2 1.3 22.9 1.7
TAIL RACE 1999 22.0 2.6 22.2 2.2 22.5 2.1 22.0 1.8 22.2 td> 1.4 22.4 1.5
SYRACUSE AIR 1997 15.0 24.6 21.1 15.5 27.0 13.3 14.6 19.1 20.4 12.0 25.9 12.1
  1998 16.0 17.3 21.3 11.6 26.3 12.6 16.0 24.2 21.8 13.2 27.4 9.3
  1999 17.8 18.8 24.0 12.9 29.9 11.6 14.6 20.2 20.6 12.2 26.4 11.5
30 YEAR AIR 1961-1990 15.0   21.3   27.6   14.3   20.2   26.1  





Table 2.

Pearson Correlation coefficients for mean, minimum daily air and Salmon River water tempetures for June, July, and August 1997-1999. Bold coefficients indicate significance at α=0.05.

    RIVER TEMP
SITE YEAR AIR-TEMP MIN MEAN MAX
DOUGLASTON 1999 MIN 0.7955 0.7532 0.6165
    MEAN 0.7316 0.8086 0.7508
    MAX 0.5424 0.7189 0.7484
BELOW 81 1997 MIN 0.8697 0.6632 0.3773
    MEAN 0.8084 0.8410 0.6559
    MAX 0.5697 0.8343 0.7910
 CO RT 2A 1997 MIN 0.6123 0.4042 0.2083
    MEAN 0.5918 0.5773 0.4811
    MAX 0.4245 0.6063 0.6338
  1999 MIN 0.7154 0.6933 0.5130
    MEAN 0.5886 0.7212 0.6597
    MAX 0.3637 0.6174 0.6779
PINEVILLE 1999 MIN 0.4079 0.5101 0.4794
    MEAN 0.3119 0.4899 0.5846
    MAX 0.1578 0.3783 0.5749
TRESTLE 1998 MIN 0.5623 0.4813 0.3672
    MEAN 0.6517 0.6281 0.5561
    MAX 0.6118 0.6489 0.6332
  1999 MIN 0.4466 0.4489 0.3923
    MEAN 0.3386 0.4097 0.4519
    MAX 0.1715 0.2950 0.4205
HATCHERY 1997 MIN 0.0588 0.0294 -0.0051
    MEAN 0.1183 0.1114 0.1057
    MAX 0.1336 0.1495 0.1723
  1998 MIN 0.4199 0.3855 0.3106
    MEAN 0.5290 0.5146 0.4438
    MAX 0.5317 0.5383 0.4834
  1999 MIN 0.2804 0.2922 0.3041
    MEAN 0.1909 0.2273 0.2728
    MAX 0.0674 0.1206 0.1878
TAIL RACE 1999 MIN 0.2365 0.2436 0.2527
    MEAN 0.1544 0.1677 0.1888
    MAX 0.0448 0.0612 0.0890





Table 3.

Species captured in Salmon River fisheries surveys.

SPECIES/SURVEY DEC-1980 EF DEC-1999 EF SUNY-ESF 1999 EF USGS/DEC 1999 SEINING
SEA LAMPREY
(AMMOCETES)
X      
AMERICAN EEL X      
STEELHEAD
(HATCHERY YEARLINGS)
X X X X
STEELHEAD
(YOY-WILD)
X X X X
ATLANTIC SALMON
(HATCHERY YEARLINGS)
      X
ATLANTIC SALMON
 (YOY-FRY STOCKING)
  X X  
BROWN TROUT (HATCHERY YEARLINGS) X      
BROOK TROUT X      
COHO SALMON (HATCHERY YEARLINGS)       X
COHO SALMON (YOY-WILD) X   X X
CHINOOK SALMON (YOY-WILD) X   X X
GRASS PICKEREL X      
CUTLIPS MINNOW X X X X
GOLDEN SHINER X     X
COMMON SHINER X   X X
BLUNTNOSE MINNOW X X X  
BLACKNOSE DACE X X X  
LONGNOSE DACE X X X  
CREEK CHUB     X X
FALLFISH X X X X
WHITE SUCKER X X X  
NORTHERN HOG SUCKER X X    
BROWN BULLHEAD X X X  
STONECAT X X    
ROCK BASS X X    
PUMPKINSEED X X    
BLUEGILL     X  
SMALLMOUTH BASS X X X  
FANTAIL DARTER X X X X
TESSELLATED DARTER X X X  
YELLOW PERCH X     X
LOGPERCH X X    





Table 4.


Fish captured in Salmon River USGS-DEC chinook seining and DEC electrofishing surveys by site, 1999

1999 USGS-DEC SEINING
1999 DEC ELECTROFISHING
SPECIES/SITE Site 1 Site 2 Site 3 Site 4 Site 1 Site 5 Site 6 Site 7 Site 8 Site 9 Site 10 Site 11 Site 12
STEELHEAD
(HATCHERY YEARLINGS)
0 0 2 182 0 0 0 0 0 0 0 0 1
STEELHEAD (YOY-WILD) 0 1 1 21 0 0 0 0 0 0 0 0 1
ATLANTIC SALMON
(HATCHERY YEARLINGS)
0 0 2 10 0 0 0 0 0 0 0 0 0
ATLANTIC SALMON
 (YOY-FRY STOCKING)
0 0 0 0 0 0 0 0 0 0 0 1 14
COHO SALMON
 (HATCHERY YEARLINGS)
0 0 2 2 0 0 0 0 0 0 0 0 0
COHO SALMON
(YOY-WILD)
0 0 1 3 0 0 0 0 0 0 0 0 0
CHINOOK SALMON
 (YOY-WILD)
364 121 405 167 0 0 0 0 0 0 0 0 0
CUTLIPS MINNOW 0 23 7 1 4 0 7 29 1 29 31 12 20
GOLDEN SHINER 0 0 1 0 0 0 0 0 0 0 0 0 0
COMMON SHINER 0 9 12 0 0 0 0 0 0 0 0 0 0
BLUNTNOSE MINNOW 0 0 0 0 0 0 0 0 0 0 12 0 0
BLACKNOSE DACE 0 0 0 0 0 0 0 0 1 0 0 0 6
LONGNOSE DACE 0 0 0 0 24 21 0 0 8 2 1 0 5
CREEK CHUB 0 7 1 0 0 0 0 0 0 0 0 0 0
FALLFISH 15 56 117 40 5 1 4 7 1 6 1 3 1
WHITE SUCKER 0 0 0 0 0 0 4 0 0 0 0 0 0
NORTHERN HOG
SUCKER
0 0 0 0 1 7 10 0 0 0 5 0 0
BROWN BULLHEAD 0 0 0 0 0 0 2 0 0 0 0 1 0
STONECAT 0 0 0 0 1 1 0 1 0 0 0 0 0
ROCK BASS 0 0 0 0 0 0 10 3 0 12 0 0 0
PUMPKINSEED 0 0 0 0 0 0 1 0 0 0 0 0 0
SMALLMOUTH
 BASS
0 0 0 0 3 0 9 1 0 2 1 2 0
FANTAIL DARTER 1 2 1 0 32 30 11 18 93 37 68 6 39
TESSELLATED
DARTER
0 0 0 0 0 0 0 0 0 0 1 0 0
YELLOW PERCH 0 0 1 0 0 0 0 0 0 0 0 0 0
LOGPERCH 0 0 0 0 2 0 0 0 0 0 0 0 0

Site 1= DOUGLASTON
Site 2= CORT 2A
Site 3= PINEVILLE
Site 4= ALTMAR
Site 5= STAIR- CASE
Site 6= MILL
Site 7= TRESTLE
Site 8= ELLIS COVE
Site 9= SCHOOL HOUSE
Site 10=
SRH-BRAID
Site 11= SRH-MAIN STEM
Site 12= UPPER FLY





Table 5.

Multiple range comparisons (pairwise t-tests) of men lengths of wild young year chinook salmon by site and date from the 1999 Salmon River USGS/DEC cooperative survey.

SITE DATE NUMBER CAUGHT NUMBER MEASURED MEAN LENGTH (mm) STD T-GROUPING1   
PINEVILLE 24-Jun-99 5 5 65.6 4.7     A  
Co RT 2A 24-Jun-99 4 4 64.3 4.8 B   A  
DOUGLASTON 24-Jun-99 12 12 60.1 7.1 B   C  
PINEVILLE 14-Jun-99 18 18 59.6 6.2 B   C D
ALTMAR 14-Jun-99 9 9 57.7 11.0 B   C D
DOUGLASTON 25-May-99 279 30 56.7 10.0     C D
PINEVILLE 02-Jun-99 220 30 55.1 7.6   F C D
PINEVILLE 07-Jun-99 45 45 54.6 8.2   F   D
Co RT 2A 14-Jun-99 37 30 54.4 8.4   F   D
DOUGLASTON 14-Jun-99 31 31 54.3 6.9   F    
DOUGLASTON 02-Jun-99 42 29 50.4 4.9   F G  
Co RT 2A 25-May-99 57 53 50.4 7.2   F G  
PINEVILLE 19-May-99 117 34 45.6 4.2 H   G  
ALTMAR 19-May-99 158 33 40.5 3.1 H      

1 - Means with the same letter are not significantly different. For example, on 24-June, mean lengths of fish measured at CO. RT. 2A were not significantly different from those measured at Pineville or Douglaston but the fish measured at Pineville were significantly longer than those measured at Douglaston.




This document is public information prepared by the The New York State Department of Environmental Conservation

Formatting © 2000 FishUSA.com