Fishery managers throughout the upper Laurentian Great Lakes are currently faced with a two-decade decline in abundance and harvest of lake whitefish Coregonus clupeaformis stocks. We used multivariate auto-regressive state-space (MARSS) models to develop long-term (90-year; 1929–2018) time-series of lake whitefish relative abundance based on commercial catch-per-effort (CPE) data for 13 statistical districts in State of Michigan waters, including 1836 and 1842 Treaty ceded waters, of Lakes Superior, Michigan, and Huron. CPE time-series were used to estimate historical baseline conditions, which were compared to more recent conditions, specifically with reference to select regulatory, environmental, and ecological conditions in each lake and fishing intensity. Population growth rates suggested that lake whitefish stocks responded: (1) negatively to high levels of harvest and expansion of sea lamprey Petromyzon marinus populations during the early-1900s; (2) positively to commercial fishery regulation and sea lamprey control during the late-1950s and early-1960s; and (3) negatively to establishment of dreissenid mussels Dreissena spp. in Lakes Michigan and Huron by 2005 and the recent period of low productivity in all three lakes since the mid- to late-2000s. When placed in a historical context, the most recent (2011–2018) lake whitefish abundances are low, intermediate, and high in 31 %, 46 %, and 23 % of all districts examined. Although environmental and ecological conditions likely drove recent declines, correlation analysis suggested that higher levels of fishing intensity were associated with greater district-specific declines in abundance during the last two decades (1999–2016), a period characterized by lower overall productivity and limited recruitment in most lake whitefish stocks.