Date of Award


Level of Access

Open-Access Thesis

Degree Name

Master of Science (MS)


Wildlife Ecology and Wildlife Conservation


Stephen Coghlan, Jr.

Second Committee Member

Joseph Zydlewski

Third Committee Member

Daniel Hayes


The Penobscot River drains the largest watershed in Maine, and once provided spawning and rearing habitats to at least 11 species of diadromous fish. The construction of dams blocked migrations of these fish and likely changed the structure and function of fish assemblages throughout the river. Further alteration to fish assemblage structure likely occurred as a result of habitat fragmentation and alteration. The proposed removal of two main-stem dams, improved upstream fish passage at a third dam, and construction of a fish bypass on dam obstructing a major tributary is anticipated to increase passage of diadromous and resident fishes. To sample fish assemblages within the lower 70 kilometers of the Penobscot River prior to dam removal, we used standardized boat electrofishing methods during both summer and fall in 2010 and 2011 while implementing two sampling designs. Fixed-station sampling on the Penobscot River was conducted at eleven pre-established 1000-meter transects. Stratified-random sampling was conducted among nine strata, at multiple randomly selected 500-meter transects within each stratum. Major tributaries were also sampled along eight fixed-station transects. In total, we captured 61,837 fish of 35 species while sampling 114 kilometers of river and tributary shoreline. Our sampling designs were equivalent in precision and efficiency for encountering species and estimating total species richness; we found no significant differences between sampling designs for the proportional abundance of all species, although the stratified-random design was slightly more efficient for characterizing proportional abundance. We combined data from both sampling designs for further analyses and identified longitudinal patterns of fish assemblage structure within the study area. Distinct fish assemblages were present among river sections bounded by dams, indicating that dams were a major driver of fish assemblage patterns within the river. Alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis) were captured frequently within the tidal river section, but at no locations upriver. Fundulus species were also abundant within the tidal river section. Smallmouth bass (Micropertus dolomieu) and pumpkinseed (Lepomis gibbosus) were most prevalent within Veazie Dam impoundment, along with the free flowing river section immediately upriver. Further upriver, warm-water species such as chain pickerel (Esox niger), brown bullhead (Ameiurus nebulosus), and yellow perch (Perca flavescens), along with cyprinid species such as common shiner (Luxilus cornutus) and fallfish (Semotilus corporalis) were more prevalent than within any other river section. Patterns of fish assemblage structure did not change considerably during our sampling; we identified relatively few species which contributed to seasonal and annual variability within the main-stem river, including smallmouth bass, white sucker (Catostomus commersoni), pumpkinseed, and golden shiner (Notemigonus crysoleucas). We predict that many anadromous fish will migrate further upriver after dam removal, potentially causing broad shifts in fish assemblage structure. Improved connectivity among habitats for many fish species could also change the longitudinal pattern of fish assemblage structure within the river. While it is difficult to predict specific changes to fish assemblages in this large river, such predictions can be tested by future studies to evaluate river rehabilitation success and the recovery of historically important fish species.