Fishing effort in the Vietnamese coastal ecosystem has rapidly increased from the 1990s to the 2000s, with unknown consequences for local ecosystem structure and functioning. Using ecosystem models that integrate fisheries and food webs we found profound differences in the production of six functional groups, the food web efficiency, and eight functional food web indices between the 1990s (low fishing intensity) and the 2000s (high fishing intensity). The functional attributes (e.g. consumption) of high trophic levels (e.g. predators) were lower in the 2000s than in the 1990s while primary production did not vary, causing food web efficiency to decrease up to 40% with time for these groups. The opposite was found for lower trophic levels (e.g. zooplankton): the functional attributes and food web efficiency increased with time (22 and 10% for the functional attributes and food web efficiency, respectively). Total system throughput, a functional food web index, was about 10% higher in the 1990s than in the 2000s, indicating a reduction of the system size and activity with time. The network analyses further indicated that the Vietnamese coastal ecosystem in the 1990s was more developed (higher ascendancy and capacity), more stable (higher overhead) and more mature (higher ratio of ascendancy and capacity) than in the 2000s. In the 1990s the recovery time of the ecosystem was shorter than in 2000s, as indicated by a higher Finn's cycling index in the 1990s (7.8 and 6.5% in 1990s and 2000s, respectively). Overall, our results demonstrate that the Vietnamese coastal ecosystem has experienced profound changes between the 1990s and 2000s, and emphasise the need for a closer inspection of the ecological impact of fishing.