This is the first study on the emergent properties for empirical ecosystem models that have been validated by time series information. Ecosystem models of the western and central Aleutian Islands and Southeast Alaska were used to examine indices of ecosystem status generated from network analysis and incorporated into Ecopath with Ecosim. Dynamic simulations of the two ecosystems over the past 40 years were employed to examine if these indices reflect the dissimilar changes that occurred in the ecosystems. The results showed that the total systems throughput (TST) and ascendancy (A) followed the climate change signature (Pacific decadal oscillation, PDO) in both ecosystems, whereas the redundancy (R) followed the inverse trend. The different trajectories for important species such as Steller sea lions (Eumetopias jubatus), Atka mackerel (Pleurogrammus monopterygius), pollock (Theragra chalcograma), herring (Clupea pallasii), Pacific cod (Gadus macrocephalus) and halibut (Hippoglossus stenolepis) were noticeable in the Finn cycling index (FCI), entropy (H) and average mutual information (AMI): not showing large change during the time that the Stellers sea lions, herring, Pacific cod, halibut and arrowtooth flounder (Atheresthes stomias) increased in Southeast Alaska, but showing large declines during the decline of Steller sea lions, sharks, Atka mackerel and arrowtooth flounder in the Aleutians. On the whole, there was a change in the emergent properties of the Aleutians around 1976 that was not seen in Southeast Alaska. Conversely, the emergent properties of both systems showed a change around 1988, which indicated that both systems were unstable after 1988.