The St. Clair-Detroit River System is located in the heart of the North American Laurentian Great Lakes, connecting lakes Huron and Erie, contributing over 90% of the inflow to Lake Erie, and providing spawning habitat for many fishes including walleye (Sander vitreus), yellow perch (Perca flavescens), and lake whitefish (Coregonus clupeaformis). Dredging and channelization have greatly altered the Detroit River thereby reducing available spawning habitat and redirecting a majority of river discharge through deep canal-like channels to offshore areas of western Lake Erie at high velocities. Fish reproduction has been measured in the Detroit River using larval surveys for over 10 years. However, quantitative estimates of contributions from spawning in the system to Lake Erie fish populations have not been determined. We use long-term biological sampling and physical habitat surveys to characterize larval drift patterns and a Bayesian approach to quantify larval export from the Detroit River. Larval export from the Detroit River into Lake Erie varied by species, across years (2006–2015), and spatially among the multiple navigational channels in the lower Detroit River. Total annual export of walleye larvae ranged from 12 million in 2013 to 114 million in 2014, yellow perch larvae ranged from 319 million in 2014 to 690 million in 2013, and lake whitefish larvae ranged from 29 million in 2010 to 84 million in 2011. Given the widespread spawning, large numbers of larvae produced, and continued system-wide water quality and aquatic habitat improvements, the Detroit River provides valuable habitat and added resilience to Lake Erie fisheries despite suffering from severe anthropogenic disturbances.