Bacteriological and physico-chemical water quality parameters were measured in rainwater from 10 harvesting tanks, belonging to two types of rainwater harvesting systems (outside tanks for garden watering and underground tanks for both outdoor and indoor uses) in Île-de-France area (France). The presence of fecal coliforms, enterococci, Pseudomonas spp., coliforms, total flora at 22°C and 36°C and total DAPI direct counts showed a microbiological contamination in water and sediment samples for both tank types. However, the harvested rainwater quality suited some existing water quality guidelines for different non-potable purposes (bathing water or reused wastewater). To our knowledge, the presence of microorganisms in sediment compartment in rainwater harvesting tank has been studied for the first time here. Results showed that the sediment could be a reservoir of re-contamination for some microbial species, which would survive in the sediment and may be resuspended in the water column. In parallel, physical-chemical parameters (temperature, turbidity, conductivity, pH and dissolved organic carbon) of collected rainwater were found in the ranges reported in the literature. Algal blooms, principally green algae, occurred in the outside tanks during spring and summer as shown by the high chlorophyll levels (the highest chlorophyll content reached 209.8 µg/L with a water pH of 9.37). Nitrate and phosphate concentrations in water samples were low (respectively less than 5 mg/L and 0.5 mg/L) but high enough to support the development of microorganisms and especially photosynthetic microorganisms in the outside tanks. The difficulty to evaluate the microbial quality of roof-harvested rainwater due to the lack of suitable quality standards is underlined. Depending on the usage of the harvested rainwater, some treatments may be needed to get a better microbial quality and direct measurements for pathogens may be also needed to establish whether or not such harvested rainwater is safe for different types of uses.