Aquaculture intensification aims to sustainably maximize the productivity of farming systems. However, increased production does not necessarily translate into greater profitability. Moreover, responses to intensification may vary among genetic groups, simultaneously affecting productive and economic performance. This study evaluated the trade-offs between productivity and profit margin in the intensive production of juvenile pirapitinga (Piaractus brachypomus), tambaqui (Colossoma macropomum), and tambatinga (Colossoma macropomum × Piaractus brachypomus) cultured in biofloc technology (BFT) and recirculating aquaculture systems (RAS). The experiment was conducted over 49 days using a completely randomized design in a 2 × 3 factorial arrangement, consisting of two production systems and three genetic groups, with four replicates per treatment. Both systems maintained suitable water quality conditions for fish culture throughout the experimental period. The RAS promoted higher final weight (41.60 vs. 31.11 g) and productivity (3.65 vs. 2.72 kg m⁻³) compared with the BFT system. In contrast, BFT reduced operational costs by approximately 31% and achieved the highest profit margins, ranging from 44.3 to 66.9%, whereas the lowest profit margin was observed for tambatinga cultured in RAS (38.9%). Among the genetic groups, pirapitinga exhibited the best productive and economic performance, followed by tambaqui, while tambatinga showed lower growth, survival, and profitability. The integrated analysis of productivity and profit margin revealed four distinct bioeconomic strategies among treatments, demonstrating that aquaculture intensification does not produce a single outcome and that productive and economic gains depend on the interaction between production system and genetic group. Overall, RAS favored production maximization, whereas BFT improved relative economic efficiency, highlighting the existence of contrasting bioeconomic strategies driven by the interaction between production system and genetic group.