Environmental, economic, and climatic changes in many parts of the world put serious pressure on water resources. Thus, a reliable alternative water supply has become a central issue on a global scale. The use of rainwater harvesting systems has emerged as one of the most efficient ways to obtain fresh water for non-potable purposes, especially in irrigation. Since there is also a universal trend of aquifer depletion, the implementation of rainwater harvesting systems will contribute to reducing the stress on conventional water resources as well as central water supply systems. While determining the suitability of the water resource, water quality becomes a prominent issue. The quality of the harvested rainwater mostly is adequate for non-potable purposes. However, due to various reasons (e.g. nutrient inputs, temperature increase, draught, etc.), cyanobacteria proliferation can occur in rainwater harvesting ponds and damage the water quality. Furthermore, some species can excrete cyanotoxins that may enter the agricultural fields by irrigation and cause environmental and public health problems. The main objective of this study was to investigate the water quality of the rainwater harvesting ponds of Istanbul which are used for irrigation. For this purpose, samples were collected from 18 rainwater harvesting ponds during the summer of 2022 and physicochemical and biological characterization of these samples was carried out. Cyanobacterial bloom was observed in 3 ponds out of 18 which the dominant species were potentially cyanotoxin producers (Microcystis, Aphanizomenon, Dolichospermum, Planktothrix, and Cuspidothrix). It is found that these ponds were not proper for irrigation purposes. To increase the water quality in these reservoirs, onsite management strategies should be taken into consideration.