A breeding colony of Little Penguins (Eudyptula minor) on Middle Island, Warrnambool, Victoria was reduced to 4 penguins in 2005 primarily due to predation by introduced foxes (Vulpes vulpes). In 2006, Maremma guardian dogs were deployed on Middle Island during the penguin breeding season to reduce predation at the declining colony. Successful protection by the Maremmas facilitated colony recovery to over 200 penguins by 2016, with management practices continually adapting to new and evolving threats. However, in recent years, increased environmental variability associated with climate change has become a rising threat, causing decreases in population size, reduced breeding success and unpredictable arrival times at the colony. This research investigates the environmental determinants driving the observed penguin responses at the Middle Island colony including variations in sea surface temperatures, Chlorophyll-a levels, and the timing and strength of the Bonney upwelling. Long-term penguin monitoring data and environmental data at varying spatial and temporal scales are used to investigate the mechanisms of influence and complex relationships between the penguin responses and environmental determinants. The subsequent capacity to predict future impacts expected at the Middle Island colony under changing climatic conditions is also explored, which may inform conservation management in an uncertain future.