Biofilms are ubiquitous in the natural environment and engineered systems. While biofilms can play a beneficial role, they also can be detrimental. For example, biofilms enable biological treatment processes such as the membrane-aerated biofilm reactor (MABR). On the other hand, biofilm can foul reverse osmosis systems, increases the energy requirements, and they can reduce the heat transfer efficiency of cooling towers, and increase hydraulic resistance of oil pipelines. The common theme is that biofilms must be properly managed. However, the mechanical properties of biofilms, which determine their development and persistence, are poorly understood. By better characterizing the mechanical properties of biofilms, better biofilm management strategies can be developed. The mechanical properties of biofilms can be used to predict biofilm response to external forces. For example, biofilms commonly develop in flowing aqueous environments, where the flow causes the biofilm to deform. Because biofilm deformation affects the flow regime, and because biofilms behave as complex heterogeneous viscoelastic materials, few models are able to predict biofilm deformation in these highly coupled systems.Biofilms have a complex matrix with heterogeneous structural and mechanical properties. This heterogeneity is commonly neglected, but may have important impacts on biofilm mechanical behavior. Considering biofilm mechanical heterogeneity in experimental and modeling studies may allow for more effective biofilm management strategies. In this study, we firstly developed a phase‐field (PF) continuum model coupled with the Oldroyd‐B constitutive equation and used this model to simulate biofilm deformation. The accuracy of the model was evaluated using two types of biofilms: a synthetic biofilm, made from alginate mixed with bacterial cells, and a Pseudomonas aeruginosa biofilm. After validating the viscoelastic PF model, the spatial distribution of biofilm non-Newtonian viscosity was considered in a second study. Image processing techniques were employed to transform the two-dimensional optical coherence tomography (OCT) biofilm image to a pixel-scaled non-Newtonian viscosity map of the biofilm. Deformation and stresses were compared for homogeneous and heterogeneous biofilm simulations. Finally, we explored the potential bias of rheometry when used to measure the mechanical properties of heterogenous biofilms. A viscoelastic biofilm model was developed using Kelvin-Voigt model, and a synthetic biofilm with layered mechanical properties was studied. In all, the results provide an important tool for predicting biofilm viscoelastic deformation with the consideration of biofilm mechanical heterogeneity. It also can benefit the design and control of biofilms in engineering systems.