Intensive microalgae cultivation systems such as High Rate Algal Ponds (HRAPs) constitute a promising way to remove macropollutants from urban wastewater. However, two sanitary issues are associated with this treatment process: the presence of pathogens that have to be inactivated and the potential aerosolisation of a high concentration of microalgae that could affect human health. Concerning pathogenic bacteria, factors affecting their inactivation in HRAPs are still not well characterized. Two pilot scale HRAPs operating under different climates (Oceanic and Mediterranean) were monitored to evaluate their capacity to remove fecal indicator bacteria (FIB) and genera containing opportunistic pathogens. Traditional plating techniques, qPCR and Illumina sequencing were combined to determine bacterial concentrations. In both HRAPs, average log10 reduction values ranged between 1 and 2 Log for FIB. The clarification of wastewater and microalgal blooming induced a sharp decrease of the FIB and of genera containing opportunistic species (Acinetobacter, Aeromonas, Arcobacter, Streptococcus). At this time, important removal was recorded for culturable FIB (4.4 and 3 Log respectively, for thermotolerant coliforms and fecal streptococci), but not noticed when using qPCR. Differences between cultural and molecular results may be due to the presence of cells in a Viable But Non-Culturable State. After the blooming period, oxygen was the main factor affecting E. coli concentration, indicating that photooxidation may play a major role in the inactivation of this bacteria in HRAPs. At the air water interface of these open water treatment processes, bioaerosols are emitted that could represent a health problem. In dedicated lab-scale instrumented aerosolisation tanks (1 m3), the capacities of microalgae from natural consortia to become airborne were compared. Is was shown that cells of Chlorella are more prone to be aerosolised that cells of Scenedesmus-like species. The effect of water temperature, biomass concentration and the presence of surfactant on aerosolisation was evaluated.