Long‐term fish community surveys were carried out in the Michigan waters of Lake Huron using bottom trawls from 1976 to 2006. Trends in abundance indices for common species (those caught in 10% or more of trawl tows) were estimated for two periods: Early (1976‐1991) and late (1994‐2006). All common species significantly decreased in abundance during the late period with the exception of the johnny darter Etheostoma nigrum and spottail shiner Notropis hudsonius, which showed no significant trends, and the round goby Neogobius melanostomus, which increased in abundance. Percentage decreases in abundance indices between 1994‐1995 and 2005‐2006 ranged from 66.4% to 99.9%, and seven species decreased in abundance by more than 90%. The mean biomass of all common species in 2006 was the lowest observed in the time series and was less than 5% of that observed in the mid‐1990s. The mean number of common species captured per trawl has also decreased since the mid‐1990s. Several factors, including recent invasion of the lake by multiple exotic species, may have contributed to these declines, but insufficient published data are currently available to determine which factors are most important. Our observations suggest that significant changes have occurred in the ecology of Lake Huron since the mid‐1990s. The extent of these changes indicates that the deepwater demersal fish community in Lake Huron is undergoing collapse.

An invasive dreissenid mussel given the working name of "quagga" has a present (spring 1993) distribution in the Laurentian Great Lakes from the western basin of Lake Erie to Quebec City. In Lake Erie, quaggas were collected as early as 1989 and now are most common in the eastern basin. In Lakes Erie and Ontario, proportions of quaggas increased with depth and decreasing water temperature. In the eastern basin of Lake Erie, quaggas outnumbered zebra mussel (Dreissena polymorpha) by 14 to 1 in deeper waters (>20 m). In Lake Ontario, quaggas were observed at depths as great as 130 m, and both quagga and zebra mussel were found to survive at depths (>50 m) where temperatures rarely exceed 5 °C. Quaggas were sparse or absent along inland waterways and lakes of New York State. Mean shell size of quagga mussel was larger than that of zebra mussel at sites in the Niagara River, Lake Ontario, and the St. Lawrence River. The largest quaggas (38 mm) were observed in the St. Lawrence River at Cape Vincent.

The alewife Alosa pseudoharengus, an invader to the Laurentian Great Lakes from the Atlantic Ocean, has been blamed for causing major disruptions of Great Lakes fish communities during the past 50 years. We reviewed the literature and examined long-term data on fish abundances in the Great Lakes to develop a new synthesis on the negative effects of alewives on Great Lakes fish communities. The results indicated that certain fish populations are substantially more vulnerable to the effects of alewives than others. More specifically, the effects of alewives on other fish populations appeared to follow a continuum—from such fishes as slimy sculpin Cottus cognatus, lake whitefish Coregonus clupeaformis, and bloater Coregonus hoyi, which were relatively unsusceptible—to Atlantic salmon Salmo salar, lake trout Salvelinus namaycush, and emerald shiner Notropis atherinoides, which were highly susceptible. Intermediate species in this continuum included yellow perch Perca flavescens, deepwater sculpin Myoxocephalus thompsonii, and burbot Lota lota. The predominant mechanism by which alewives exerted their negative effect appeared to be predation on the larvae of other fishes. The key factor in the extirpation of Atlantic salmon from Lake Ontario, however, was probably early mortality syndrome induced by a diet rich in alewives. We conclude that the degree of restoration of the native Great Lakes fish community depends in part on the degree of control of the alewife population.

Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log₁₀ 4.8–6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs.

Ecosystem change often affects the structure of aquatic communities thereby regulating how much and by what pathways energy and critical nutrients flow through food webs. The availability of energy and essential nutrients to top predators such as seabirds that rely on resources near the water's surface will be affected by changes in pelagic prey abundance. Here, we present results from analysis of a 25‐year data set documenting dietary change in a predatory seabird from the Laurentian Great Lakes. We reveal significant declines in trophic position and alterations in energy and nutrient flow over time. Temporal changes in seabird diet tracked decreases in pelagic prey fish abundance. As pelagic prey abundance declined, birds consumed less aquatic prey and more terrestrial food. This pattern was consistent across all five large lake ecosystems. Declines in prey fish abundance may have primarily been the result of predation by stocked piscivorous fishes, but other lake‐specific factors were likely also important. Natural resource management activities can have unintended consequences for nontarget ecosystem components. Reductions in pelagic prey abundance have reduced the capacity of the Great Lakes to support the energetic requirements of surface‐feeding seabirds. In an environment characterized by increasingly limited pelagic fish resources, they are being offered a Hobsonian choice: switch to less nutritious terrestrial prey or go hungry.