<jats:p>Abstract. A model of the radionuclide accumulation in fish taking into account the contribution of different tissues and allometry is presented. The basic model assumptions are as follows. (i) A fish organism is represented by several compartments in which radionuclides are homogeneously distributed. (ii) The compartments correspond to three groups of organs or tissues: muscle, bones and organs (kidney, liver, gonads, etc.) differing in metabolic function. (iii) Two input compartments include gills absorbing contamination from water and digestive tract through which contaminated food is absorbed. (iv) The absorbed radionuclide is redistributed between organs or tissues according to their metabolic functions. (v) The elimination of assimilated elements from each group of organs or tissues differs, reflecting differences in specific tissues or organs in which elements were accumulated. (vi) The food and water uptake rates, elimination rate, and growth rate depend on the metabolic rate, which is scaled by fish mass to the 3/4 power. The analytical solutions of the system of model equations describing dynamics of the assimilation and elimination of 134Cs, 57Co, 60Co, 54Mn and 65Zn, which are preferably accumulated in different tissues, exhibited good agreement with the laboratory experiments. The developed multi-compartment kinetic–allometric model was embedded into the box model POSEIDON-R (Maderich et al., 2018b), which describes transport of radionuclides in water, accumulation in the sediment and transfer of radionuclides through the pelagic and benthic food webs. The POSEIDON-R model was applied for the simulation of the transport and fate of 60Co and 54Mn routinely released from Forsmark Nuclear Power Plant (NPP) located on the Baltic Sea coast of Sweden and for calculation of 90Sr concentration in fish after the accident at Fukushima Dai-ichi NPP. Computed concentrations of radionuclides in fish agree with the measurements much better than calculated using standard whole-body model and target tissue model. The model with the defined generic parameters could be used in different marine environments without calibration based on a posteriori information, which is important for emergency decision support systems.</jats:p>