On-line performance indicators of a microalgae-bacteria consortium were screened out from different variables based on pH and dissolved oxygen on-line measurements via multivariate projection analysis, aiming at finding on-line key state indicators to easily monitor the process. To fulfil this objective, a pilot-scale high-rate pond for urban wastewater treatment was evaluated under highly variable conditions, i.e. during the start-up period. The system was started-up without seed of either bacterial or microalgal biomass. It took around 19 days to fully develop a microalgal community assimilating nutrients significantly. Slight increases in the biomass productivities in days 26–30 suggest that the minimum time for establishing a performant bacteria-microalgae consortium could be of around one month for non-inoculated systems. At this point, the process was fully functional, meeting the European discharge limits for protected areas. The results of the statistical analyses show that both the pH and the dissolved oxygen concentration represent accurately the biochemical processes taking place under the start-up of the process. Both pH and dissolved oxygen represented accurately also the performance of the high-rate algal pond, being affordable, easily-implemented, options for monitoring, control and optimization of industrial-scale processes.