This research is aimed at understanding the reactor‐settler interaction. The reactor operating conditions affect the sludge‐settling properties due to (a) production of exocellular polymer that serves as a flocculant in the settler and (b) population shift from flocculating bacteria to filamentous microorganisms that do not settle. A structured kinetic model that accounts for stored substrate and production of polymers, biomass, and inerts was constructed and applied to various open and closed reactor configurations. It is based on our observation that, in a batch reactor, the polymer is produced during endogenous respiration. The model describes well the observed temporal variation in substrate, biomass, and polymer concentration. Application of the model to continuous operation predicts increasing polymer concentration with sludge age, which is in good agreement with one study in the literature. Our study in a once‐through reactor, as well as others, suggests an inverse dependence. The difference is probably due to different operating modes. Our study confirmed the role of the polymer in the sedimentation process. Under some conditions, however, a slow population shift to filamentous growth becomes the dominant factor.