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In the early 1990s, ecological and fishery data from the Gulf of Nicoya (Pacific Ocean) were holistically analyzed, and a trophic model was constructed using the Ecopath modeling approach. The results indicated that this tropical estuary, which is a Costa Rican fishery hot spot, was already overexploited by shrimp trawlers and the longline fleet, and recent observations suggest further deteriorations in this system. To evaluate the ecosystem and socioeconomic changes in the Gulf of Nicoya over the last 20years, the 1993 model was reconstructed with data from 2013 to compare both system states. Although the summary statistics of both states (i.e., 1993 and 2013) suggested that the system maintained its general functionality and even enabled the total harvest to increase by approximately 20%, a more detailed analysis of the levels of the functional groups suggested that the system was further degraded as follows: (1) most shrimp, eel, and catfish species decreased their share in the catches, with severe economic losses for the fishery; (2) of the species that substantially increased their share in the catches, most were short-lived, low-value species, such as small pelagic and small demersal fishes; and (3) catches of long-lived, high-trophic-level fish, such as rays, sharks, mackerels, and barracudas, decreased. A picture emerged in which the advancing fishery of low-trophic-level species with low economic value enabled the total harvest to increase, while valuable shrimp resources and higher-trophic-level species were depleted. These developments caused a tremendous economic loss of approximately 50%.