Policies aiming to restore ecosystems, achieve thriving fisheries and reverse biodiversity loss require knowledge of their former status and long-term variation. As quantitative fish data is typically only available for recent decades long after changes may have occurred, a greater use of qualitative sources has been encouraged in marine historical ecology. We examined diverse historical information (including maritime history, fisheries reports, naturalists' accounts, recipes, nautical charts and newspapers) across a multi-century time span (13th–20th century) for a wide range of species to document their long-term trajectories in an understudied Northeast Atlantic ecosystem (Irish Sea coast of Wales). We find strong evidence of the loss of both a pelagic fishery for herring, which was of fundamental socio-ecological importance since at least the 13th century, and the loss of significant multi-species demersal and intertidal fisheries. Local, commercial and/or functional extinction has occurred for taxa spanning a wide range of diversity (crustacean, elasmobranchs, sturgeon, and teleosts), body size and ecological role, suggesting far-reaching changes to food webs. This raises fundamental questions about the present-day health and integrity of this coastal ecosystem and the long-term viability of current fisheries which depend on a few shellfish species. Our century-scale synthesis of qualitative data for multiple taxa allows the collective breadth of losses to be fully appreciated and may reduce the risk of ‘shifting baselines’. Restoration to historical baselines may not be achievable, but our findings provide evidence of long-term change relevant to policies for recovery, and prevention of further decline of fishes, fisheries and ecosystems.