Abstract Population models are increasingly being used to extrapolate individual-level effects of chemicals, including metals, to population-level effects. For metals, it is also important to take into account their bioavailability to correctly predict metal toxicity in natural waters. However, to our knowledge, no models exist that integrate metal bioavailability into population modeling. Therefore, our main aims were to 1) incorporate the bioavailability of copper (Cu) and zinc (Zn) into an individual-based model (IBM) of rainbow trout (Oncorhynchus mykiss), and 2) predict how survival-time concentration data translate to population-level effects. For each test water, reduced versions of the general unified threshold model of survival (GUTS-RED) were calibrated using the complete survival-time concentration data. The GUTS-RED individual tolerance (IT) showed the best fit in the different test waters. Little variation between the different test waters was found for 2 GUTS-RED-IT parameters. The GUTS-RED-IT parameter “median of distribution of thresholds” (mw) showed a strong positive relation with the Ca2+, Mg2+, Na+, and H+ ion activities. Therefore, mw formed the base of the calibrated GUTS bioavailability model (GUTS-BLM), which predicted 30-d x% lethal concentration (LCx) values within a 2-fold error. The GUTS-BLM was combined with an IBM, inSTREAM-Gen, into a GUTS-BLM-IBM. Assuming that juvenile survival was the only effect of Cu and Zn exposure, population-level effect concentrations were predicted to be 1.3 to 6.2 times higher than 30-d laboratory LCx values, with the larger differences being associated with higher interindividual variation of metal sensitivity. The proposed GUTS-BLM-IBM model can provide insight into metal bioavailability and effects at the population level and could be further improved by incorporating sublethal effects of Cu and Zn. Environ Toxicol Chem 2021;40:2764–2780. © 2021 SETAC