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Although the Tonle Sap Lake is the largest natural inland lake in Southeast Asia, little is known about the spatio-temporal patterns of its composition and yields. The present paper aimed to investigate the temporal change of yields of the most dominant fish species and to evaluate the spatio-temporal changes in the fish community and the indicator species of assemblages. Fish catch data were collected from thirty-three fishing lots around the lake during the open season from October to May each year between 1994 and 2000. The fish yields were dominated by few commercial fishes: Channa micropeltes, Pangasianodon hypophthalmus, Channa striata, Cyclocheilichthys enoplos, Henicorhynchus spp., Barbonymus gonionotus, Micronema spp. and Trichopodus microlepis. The standard linear regression coefficients of the fish yields versus year were negative for all these commercial species except T. microlepis. Moreover, the total fish yields of the lake were temporally declined (standard coefficient = −2.410, adjusted r2 = 0.272). Nonmetric multidimensional scaling of the fish assemblage data showed a clear opposition between northern assemblage and southern assemblage along the first axis, and the temporal pattern of the samples from 1994 to 1999 was explained by the second axis. The fish species assemblage from earlier years (1994 and 1995) was characterised by the abundance of all functional groups of black-white-grey fish species, but more recent years (1996–1999) were linked to white and grey functional groups, which was explained by a decrease in many black fishes.