1999 Monitoring Report TILLAMOOK BAY FISH USE OF THE ESTUARY Prepared for The Tillamook Bay National Estuary Project And Tillamook County Cooperative Partnership Garibaldi, Oregon Prepared by Robert H. Ellis, Ph. D. Ellis Ecological Services, Inc 20988 S. Springwater Rd. Estacada, Oregon 97023 October 22, 1999 SUMMARY In 1999, a Comprehensive Conservation and Management Plan (CCMP) was completed for the Tillamook Bay watershed. The CCMP lays out a variety of management actions designed, in part, to achieve the goal of protecting and restoring estuarine habitat for improvement of the fishery resources of Tillamook Bay and its watershed. Baseline information on the present status of the estuary's fish community and periodic updating of the baseline information through monitoring were identified as essential for evaluation of the CCMP's management actions. This study was conducted to describe the present status of the fish community in Tillamook Bay and to design and test a long-term monitoring strategy for fish. The study was conducted during the summer and autumn of 1998 and the spring and summer of 1999. The fish sampling done in 1998 was used to provide an estuary-wide overview of the fish species composition and relative abundance during the mid-summer period and to test sampling gear and sampling strategies for development of a long-term monitoring program. The sampling conducted in 1999 built upon the information gained in 1998 and provided an initial test of a sampling design for long-term monitoring of the Bay's fish community. Current fish use of the estuary was described by updating the comprehensive fish survey data collected by Oregon Department of Fish and Wildlife (ODFW) during the mid- 1970s. The objective was to obtain sufficient information on present conditions so that comparisons could be drawn between the two studies in terms of species richness, relative abundance of common species, distribution of common species, frequency of capture by similar sampling gear, and monthly trends in catch per effort. Sampling of the fish community in 1998 was conducted using beach seine, bottom trawl, fyke net and round-haul net. During 1999, initial testing of the proposed long-term monitoring program was conducted using beach seine, trawl and fyke nets. Sampling was conducted during daylight hours throughout the saline portions of the estuary, including the salt marsh habitat at the southern end of the Bay. Species Composition: A total of 40 fish species were collected during this study whereas a total of 59 species were captured during ODFW's surveys during the mid- 1970s. Of the 40 species captured in this study, all but four were present in the mid- 1970s. Seven families and 23 species found in the mid-1970s were not captured in this study. All of the missing species were relatively rare in ODFW's catch with none comprising more than 0.1 percent of the total catch. It is considered likely that the differences in species composition can be explained in terms of sampling effort rather than intrinsic changes in the fish community. ODFW sampled monthly at 28 sampling locations over a 2.5-year period and conducted 1,239 trawl and 465 beach seine sets. In this study, sampling was limited to five months in 1998 and four months in 1999. A total of 30 trawl, 120 beach seine sets and 17 round-haul net sets were made. vi Relative Abundance: Eight of the ten most abundant species present in the mid-1970s were among the ten most abundant species captured in this study. In both studies the ten most abundant species comprised over 95 percent of the total catch. The ten most abundant species in this study in order of abundance were Pacific staghorn sculpin, surf smelt, shiner perch, English sole, Pacific herring, chum salmon, chinook salmon, Pacific sanddab and starry flounder. The abundant species present in ODFW's mid-1970s catch but in relatively low abundance in this study were Northern anchovy and rockfish spp. Differences between the studies in the abundance of Northern anchovy can probably be explained by normal wide fluctuations in their use of the estuary. The differences seen between the studies in juvenile rockfish abundance are not as easily explained. During their 2.5-year study in the mid-1970s ODFW, collected 1,267 juvenile rockfsh. Only one juvenile rockfish was collected in this study. Since sampling was conducted in the same areas and during the same season as in the ODFW study, we conclude there is reason to be concerned that juvenile rockfish use of the estuary has substantially declined since the mid-1970s. General Pattern of Distribution and Abundance: All but one of the abundant species in the beach seine catch were found throughout the estuary. The exception was Pacific sandlance, which occurred only in the mid- and lower regions of the Bay. Total beach seine catch per effort was about the same during 1999 in the upper (100.8 fish per seine) and lower (106.4 fish per seine) regions of the estuary. The mid-region of the estuary had the lowest (65.1 fish per seine) beach seine catch per effort. This distribution in catch per effort reflects conditions in the spring and summer months and is probably not indicative of the annual pattern of abundance in the estuary. Pacific staghorn sculpin was the most frequently caught species throughout the estuary. Schooling species such as surf smelt, shiner perch, Pacific herring and Pacific sandlance occurred relatively infrequently in the catch but numbers were relatively high when they were caught. Trawling in the subtidal channel habitat in the lower bay yielded a number of marine species that were not captured in the beach seine. For example, cabezon, eel pout, tom cod, sand sole and rock prickleback were only captured in the trawl. Overall, the general distribution of fish species found in this study was very similar to that found in the mid-1970s. Use of the Estuary by Anadromous Salmonids: All five species of anadromous salmonids known to occur in the Tillamook Bay watershed were collected during this study. However, only juvenile chum and chinook salmon were caught in any abundance. Chum salmon fry were present in the catch from late March through June 1999, with peak abundance in the beach seine in late April. Growth of chum fry was rapid with increases in length from about 45 mm to 90 mm by the end of June. Juvenile chinook salmon entered the beach seine catch in mid-June 1999 and were most abundant in the late July samples. Relatively small numbers of coho salmon fry and smolt were found in the estuary from May through mid June, primarily near the mouths of the Kilchis, Miami and Trask Rivers. Sea-run cutthroat trout, ranging in length 140 to 400 mm,were captured primarily in the lower bay at Hobsonville Point and in the upper bay near the mouth of the Kilchis River. Only six steelhead trout were caught. They were relatively large juveniles, ranging in size from 281 to 378 mm in length. vii In late April, we collected 462 chum salmon fry in beach seine samples. Five of the fry had caudal fin clips, indicating that they had been captured at ODFW's downstream monitoring site on the Little North Fork Wilson River in March or April 1999. Using the ratio of fin clipped fish in our sample and in ODFW's estimate of total fry outmigrants by late April along with assumptions regarding rates of downstream movement, it was estimated that as many as one-half of the fry present in our samples may have origninated from the Little North Fork Wilson River. This result was surprising in that the Little North Fork Wilson River represents only a small percentage of the total chum salmon spawning habitat in the watershed. Overall, the relative abundance of salmonids in this study was similar to that found in the mid-1970s. Chum and chinook salmon were the only abundant salmonids in the mid- 1970s catch. Abundance comparisons between the studies could not be made due to differences in sampling gear. Use of the Estuary by Non-Salmonid Species: The most abundant non-salmonid species in the estuary were euryhaline marine species. Temporal cycles in the composition, abundance and distribution of these species are largely influenced by seasonal spawning migrations, reproductive cycles and the recruitment of large numbers of juvenile fishes that use the estuary as a nursery ground. Information on beach seine catch per effort and on length frequency distribution of Pacific staghorn sculpin, surf smelt, shiner perch, English sole, Pacific herring and starry flounder indicates that juvenile rearing is the primary use of the estuary. However, some species such as shiner perch, starry flounder, and Pacific staghorn sculpin also use the estuary for spawning. Both similarities and difference in the seasonal pattern of beach seine catch per effort were found between this study and ODFW's mid-1970s study. Most of the difference could be explained in terms of differences in sampling gear efficiency for small individuals. Environmental Relationships: Catch per effort for eight of the most abundant species in the 1999 beach seine catch was plotted against salinity measured at time of capture. Salinity appeared to influence the distribution of several species. Pacific herring, English sole and surf smelt were found primarily in relatively high salinities. Juvenile chinook salmon, although found throughout the estuary, also appeared to prefer the higher salinities of the lower estuary. Starry flounder were most abundant in lower salinity water. Pacific staghorn sculpin and shiner perch distribution indicated a broad salinity tolerance. A 2-way analysis of variance (ANOVA) was used to compare mean number of species on rocky shoreline habitat with fine grained (sand and fine silty/sand) habitat.