This paper outlines an approach to the development of computational models of cells for marine environmental toxicology. Exposure of cells to pollutants can lead to lysosomal damage and dysfunction, augmented autophagy, cellular dysfunction and atrophy and ultimately tissue pathology and organ damage. The application of carbon and nitrogen based models of intra cellular vesicular traffic for simulating the autophagic and lysosomal response of the hepatopancreatic digestive cells of marine molluscs is described. Two numerical models of the vesicular transport of carbon and nitrogen in the cell are presented. These demonstrate the importance of endocytotic uptake as a driver of lysosomal dynamics and the need to recognize and model it as a discrete process. Conceptual and mathematical models of the toxic impact of polycyclic aromatic hydrocarbons on the digestive gland are presented. The role of experimental research and the need to integrate it with modelling is highlighted.