A previous study documented a correlation between Atlantic Cod (Gadus morhua) recruitment in the Gulf of Maine and an annual index of the north component of May winds. This correlation was supported by modeling studies that indicated unusually strong recruitment of Gulf of Maine Atlantic Cod results from high retention of spring-spawned larvae in years when winds were predominately out of the north, which favor downwelling. We re-evaluated this relationship using updated recruitment estimates and found that the correlation decreased between recruitment and wind. The original relationship was largely driven by two recruitment estimates, one of which (2005 year class) was highly uncertain because it was near the terminal year of the assessment. With additional data, the updated assessment estimated lower recruitment for the 2005 year class, which consequently lowered the correlation between recruitment and wind. We then investigated whether an environmentally-explicit stock recruit function that incorporated an annual wind index was supported by either the original or updated assessment output. Although incorporation of the annual wind index produced a better fitting model, the uncertainty in the estimated parameters and the implied unexploited conditions were not appropriate for providing management advice. These results suggest the need for caution in the development of environmentally-explicit stock recruitment relationships, in particular when basing relationships and hypotheses on recruitment estimates from the terminal years of stock assessment models. More broadly, this study highlights a number of sources of uncertainty that should be considered when analyses are performed on the output of stock assessment models.