In wastewater treatment technologies, employing biofilms or granular biomass, processes might occur at very different spatial and temporal scales. Model development for such systems is typically a tedious, complicated, and time consuming task, which involves selecting appropriate model equations for the different scales, making appropriate and simplifying assumptions, connecting them through a defined linking scheme, analyzing and solving the model equations numerically, and performing parameter estimations if necessary. In this study, a structured framework for modeling such systems is developed. It aims to support the user at the various steps and to reduce the time it takes to generate a model ready for application. An implementation of the framework is illustrated using a simple case study, which considers treatment of a nitrogen-rich wastewater via nitritation.