To date, computational fluid dynamics (CFD) models have been primarily used for evaluation of hydraulic problems at wastewater treatment plants (WWTPs). A potentially more powerful use, however, is to simulate integrated physical, chemical and/or biological processes involved in WWTP unit processes on a spatial scale and to use the gathered knowledge to accelerate improvement in plant models for everyday use, that is, design and optimized operation. Evolving improvements in computer speed and memory and improved software for implementing CFD, as well as for integrated processes, has allowed for broader usage of this tool for understanding, troubleshooting, and optimal design of WWTP unit processes. This paper proposes a protocol for an alternative use of CFD in process modelling, as a way to gain insight into complex systems leading to improved modelling approaches used in combination with the IWA activated sludge models and other kinetic models.