A better understanding of the fate of commercial pellets and natural resources in semi-intensive aquaculture can help to reduce environmental impacts as well as the overall costs of production in pond production systems. However, in these mixed systems, trophic structures can be complex. Here, we investigated the trophic web structure in Indonesian giant gourami (Osphronemus goramy) aquaculture ponds based on the analysis of the values of stable carbon and nitrogen isotopes (δ13C and δ15N) in 10 pond components of different trophic levels (i.e. plankton of different sizes, macroinvertebrates, periphyton, fish, sediment and commercial pellets). Isotope niche spaces (standard ellipse areas) were calculated for giant gourami at the beginning (month 0), the middle (month 3) and the end (month 5) of the trial. Our results showed that commercial pellets were the primary diet source for giant gourami throughout the 152-day trial in ponds. Nevertheless, differences in 15N and trophic niche sizes at month 0, month 3 and month 5 suggested slight changes in the giant gourami diet during the trial. Altogether, our results highlight that, in a typical omnivorous species reared in semi-intensive pond conditions, the endogenous resources of the pond are barely utilized and the diet is mainly based on commercial pellets. Such findings highlight the need of optimizing the use of both natural pond resources and commercial pellets.