This paper describes results from a mathematical modelling based study of fluid flow and heat transfer phenomena in the melting and delivery ends of an oxy-fuel fired glass furnace. The three-dimensional mathematical model used in this study not only integrates phenomena taking place in the various sub-domains (i.e. batch, combustion and melt in the melter) of the two sections, it also integrates the two sections themselves. The model was used to study the impact of bubbling on flow and heat transfer phenomena and glass quality. The integration of the melting and delivery ends made it possible to relate glass quality parameters (e.g. the stones) in the delivery end to specify locations where the stones originate on the melter surface.