Over the past several years, Indonesian freshwater aquaculture has intensified, with a concomitant increase in the use of commercial pellets. To assess the effects of pond aquaculture intensification on nutrient dynamics, we monitored nutrients and fish production in a small-scale fish farm in West Java province. The studied system consisted of semi-intensive giant gourami (Osphronemus goramy) production in four small earthen ponds (353–482 m2 each and 0.46–0.55 m deep). Nitrogen (N) and phosphorus (P) fluxes through the ponds were monitored, and data on fish production were collected during a 5-month production cycle. Results showed that, on average, 61% total N and 77% P inputs were trapped in the accumulated sediments. Only 15% of total N and <3% P inputs introduced into ponds were recovered in harvested fish. Sediment nutrient accumulation increased linearly with total nutrient input. The consequences of intensification of giant gourami aquaculture using this production model are explored in terms of nutrient use efficiency and environmental impact.