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Due to the environmental problem of climate change, it has been forecasted that the Hawaiian islands can expect increased drought and increased rainfall variability. This could cause a change in stream flow and threaten the amphidromous waterfall climbing gobies, Sicyopterus stimpsoni. To study the impact of these projected changes, we used spatially-explicit, individual-based population models with four levels drought and three levels of rainfall variability for three islands with different topographies (Hawai'i, O'ahu and Kaua'i) and looked at the effect on the goby population dynamics after 10 years. Our results showed that total abundance was impacted by drought, variability, and island shape, especially under extreme conditions. The rate of morphological change and percent of juveniles was also negatively affected by the extreme conditions. Overall, the populations were stable under moderate drought conditions, but suffered when conditions reached extreme levels.