Knowledge of stock—recruitment dynamics is as important for control of pest species such as the sea lamprey (Petromyzon marinus) as it is for sustainable harvest management of exploited fish species. A better understanding of spatial and temporal variation in recruitment of pest populations may inform managers on where and when to effectively apply different control methods. Sea lamprey stock—recruitment data combined from streams across the Great Lakes basin into a Ricker stock—recruitment model indicated both compensation (density-dependent survival) and a large amount of density-independent recruitment variation. We evaluated the use of a mixed-effects model to look at common year effects and stream-level variables that could affect productivity and growing season length, with the objective of identifying factors that may explain this density-independent variation in recruitment. After selecting the “best model”, we tested factors that might affect recruitment variation, using a Great Lakes dataset comprising 97 stream— years. Lake Superior tributaries, streams with larger numbers of lamprey competitors, and streams regularly requiring lampricide treatment showed significantly higher recruitment. Alkalinity and thermal regulation did not affect the observed recruitment pattern among streams. In four long-term study streams we observed significant variation among streams, tested as a fixed effect, but no evidence suggested a common pattern of variation among years. Differences in recruitment among streams were consistent with evidence of quality of spawning and larval habitat among streams. Our findings suggest that management models should account for differences in recruitment dynamics among sea lamprey-producing streams, but not common year effects.