Capture‐based aquaculture (CBA) is a strategy to capture wild aquatic organisms for rearing. The most iconic species produced under this scheme are bluefin tunas. In Mexico, CBA of this species is developed with Pacific bluefin tunas (PBFT). The parametrization of a biological production function able to describe biomass dynamics during the production cycle is one of the strategies that can help optimize production. The objective of this study was to explain biomass dynamics in capture‐based Pacific Bluefin tuna aquaculture in Mexican waters through parameterization of a growth and survival model. This study also assessed the impact of uncertain intrinsic CBA variables (i.e. seed weight, number of stocked individuals and sea surface temperature [SST] variability). The model was parameterized with production records of 47 net pens in two production sites (an offshore and an inshore facility) during three cycles. The results suggested that production performance was related to SST given that this factor affected survival, mainly during the first ≈40 days after stocking. The risk analysis showed that stocking during the second half of the fishing season from June to August increased the likelihood of matching or exceeding the Key Performance Indicator (KPI) defined regarding biomass increase per pen.