Environmental regimes set the timing and location of early life-history events of migratory species with synchronised reproduction. However, modified habitats in human-dominated landscapes may amplify uncertainty in predicting recruitment pulses, impeding efforts to restore habitats invaluable to endemic species. The present study assessed how environmental and spawner influences modulate recruitment variability and persistence of the Missouri River shovelnose sturgeon (Scaphirhynchus platorynchus) under modified seasonal spawning and nursery habitat conditions. Using a spatially explicit individual-based biophysical model, spawning cycle, early life-history processes (dispersal, energetics and survival) and prey production were simulated under incrementally perturbed flow (from –10 to –30%) and temperature (+1 and +2°C) regimes over 50 years. Simulated flow reduction and warming synergistically contracted spring spawning habitats (by up to 51%) and periods (by 19%). Under these conditions, fewer mature females entered a reproductive cycle, and more females skipped spawning, reducing spawning biomass by 20–50%. Many spawners migrated further to avoid increasingly unfavourable habitats, intensifying local density dependence in larval stages and, in turn, increasing size-dependent predation mortality. Diminished egg production (by 20–97%) and weakened recruitment pulses (by 46–95%) ultimately reduced population size by 21–74%. These simulations illustrate that environmentally amplified maternal influences on early life histories can lower sturgeon population stability and resilience to ever-increasing perturbations.