Production of valuable marine resources is threatened by chronic underestimation of fisheries impacts. Over-exploitation has caused a decline in many traditional food fish and enabled replacement by historically undervalued species. I analyzed federal survey data to identify understudied species encountered by trawl fishing gear and found the majority of captured species lack population assessments and/or catch regulations. There are substantially higher total numbers of encountered species and, in turn, higher percentages of understudied species (up to 95%) in the southern regions potentially following the latitudinal biodiversity gradient. This critical gap in understanding coastal marine ecosystems, which will be more significant in global fisheries that lack infrastructure or have high biodiversity, undermines ecosystem-based management and sustainability of fisheries. Ecosystem-based fisheries management (EBFM) is intended to address all aspects of the ecosystem, yet most regions still lack knowledge regarding most species, and consequently, the interactions between most species. Northwestern Atlantic ecosystems are in flux with evidence of community and potential regime shifts, and focusing management and research efforts on economically-important species or those with presumed ecological value limits the understanding and monitoring of these changes. To address this large knowledge gap within the Northeast U.S., I identified regional population trends among commonly encountered species that lack stock assessments using data from the National Marine Fisheries Service fishery-independent surveys conducted since 1963 in the Gulf of Maine, Georges Bank, and Southern New England, and 1967 in the Mid-Atlantic Bight. Breakpoint analysis was used to estimate the number of species with positive or negative trends in abundance in recent years. Further, I related species rankings of vulnerability and resilience to determine possible relationships between abundance trends and life history characteristics. Lastly, I determined whether the surveys had the necessary power to detect critical population declines over periods of 10, 15 and 30 years based upon the variance in the abundance calculated from the existing survey data. The results demonstrated the lack of power of the NMFS survey to detect trends in the majority of understudied species, although up to four out of 104 trends may have adequate power to be monitored without further investment. Government agencies should strive to increase power through increased investment in biological sampling programs and enhancing survey design. Trends between assessed and non-assessed species were similar, indicating that commercial species trends may act as a proxy for those that are not. Significant uncertainty exists in these analyses and the critical gap in the knowledge of our coastal systems suggest precautionary management strategies that include spatial management, enhanced gear technologies, increased numbers of stock assessments, and collaboration amongst stakeholders and managers are required to incorporate the understudied species component into EBFM.