This chapter addresses some of the challenges associated with trying to model population fluctuations, bloom formation and collapse of planktonic cyanobacteria. It is argued that improved modelling and prediction rely on a better understanding of the physiological responses of cyanobacteria to the physical and chemical characteristics of their environment. In addition there is a need to understand better the complex trophic interactions that influence population dynamics. The high variability of cyanobacterial populations represents a major challenge for models attempting to make predictions at the whole lake scale. Many of the physiological attributes described within specific models do not capture the dynamics of cyanobacteria, because of the extensive parameterisations required by the array of descriptive algorithms. The physiological attributes to be modelled include the ability to fix nitrogen, store both nitrogen and phosphorus, capture light across a range of wavelengths with specific accessory pigments, form colonies or filaments and regulate buoyancy through the balance between gas vacuoles and cellular constituents.