Integrated algal pond systems (IAPSs) combine anaerobic and aerobic bioprocesses to affect sewage treatment. The present work describes the isolation and partial characterisation of soluble extracellular polymeric substances (EPSs) associated with microalgal bacterial flocs (MaB-flocs) generated in high rate algal oxidation ponds (HRAOPs) of an IAPS treating domestic sewage. Productivity and change in MaB-flocs concentration, measured as mixed liquor suspended solids (MLSS) between morning (MLSSAM) and evening (MLSSPM) were monitored and the substructure of the MaB-flocs matrix examined by biochemical analysis and Fourier transform infrared spectroscopy (FT-IR). Results show that MaB-flocs from HRAOPs are assemblages of microorganisms produced as discrete aggregates as a result of microbial EPS production. Formation and accumulation of the EPS was stimulated by light. Analysis by FT-IR revealed characteristic carbohydrate enrichment of these polymeric substances. In contrast, FT-IR spectra of EPSs from dark-incubated MaB-flocs confirmed that these polymers contained increased aliphatic and aromatic functionalities relative to carbohydrates. These differences, it was concluded, were due to dark-induced transition from phototrophic to heterotrophic metabolism. The results negate microalgal cell death as a contributor to elevated chemical oxygen demand of IAPS treated water.