© 2019 Elsevier Ltd From fall 2013 through 2015, a large-scale, multi-year warm water anomaly occurred in the northeast Pacific Ocean. The phenomenon had negative impacts on some oceanic predators, including higher mortalities and poor body conditions. We studied the effect of this warm water anomaly on the weight gain of Guadalupe fur seal (Arctocephalus philippii townsendi) neonates off the coast of the Baja California Peninsula, Mexico. Individuals were captured, marked, and weighed every 13–15 days, up to 60 days of age, during the early nursing seasons (mid-June to mid-August) of 2014–2016 at this subspecies’ only reproductive colony, located on Guadalupe Island. The body weight was measured at each capture and recapture. A hierarchical Bayesian model was used to explore the impact of sea surface temperature (SST) anomalies on the neonates’ weights. The hierarchical structure included connected models for the spring-summer SST trend around the colony, the neonatal body weight gain with age, and the relationship between the anomalies of both variables. Marked neonates were also tracked in order to estimate survival rates during first two months of age. Overall, positive SST anomalies had a negative effect on neonatal body weight gain. The northeast Pacific Marine Heatwave precipitated the lowest weights at birth and the slowest weight gain in 2014, as well as low weights and the lowest survival rate in 2015, likely due to the persistence of the warm anomalies. The evident sensitivity of Guadalupe fur seal neonates to regional warming conditions highlights their vulnerability under scenarios of climate change, which could impede this subspecies’ continued recovery from near extinction.