Microalgae grown in photo-bioreactors can be a valuable source for biomass especially when combined with the treatment of wastewater. While most published research has been studying pure cultures, consortia of algae and bacteria from the wastewater have more complex dynamics affecting both the biomass production and pollutant removal. In this paper we investigate dynamics of algal and bacterial communities in mixed culture photo-bioreactors using chlorophyll and real-time PCR analysis. Wastewater photo-bioreactors were inoculated with water from a nearby lake to add native algae species. The results indicated a decline in bacterial 16S rDNA copy numbers before algae started to multiply. The photo-bioreactors inoculated with lake algae produced more biomass and grew faster than the algae originating only from wastewater. The reactors were effective in removing ammonia from the wastewater which seemed work to mostly through nitrification thus causing an increase in nitrate concentration. There was also an increase in Cr, Co and Ni ion concentrations during the experiment suggesting they may have moved from organic complexes to the water phase as free ions.