This study aims to assess the capabilities of the advanced two-dimensional water quality and hydrodynamic model CE-QUAL-W2 v4.5 sediment diagenesis module, focusing on its application to a reservoir in Portugal over a six-year period (2016–2021). Overall, the results suggest that the diagenesis model is better suited for detailed process-based dynamics over extended timeframes, whereas simpler models such as the Hybrid model (combining the zero- and first-order models), are more appropriate for short- to medium-term applications or situations with limited data availability.