Sustainability of irrigation systems is crucially important for both economical and efficient usage of natural water sources. Irrigation system efficiency could be negatively affected by some natural flora such as micro (Arthrospira maxima) and macro (Cladophora sp.) algae. In this study, efficiency of UV-C radiation, which has been proven effectiveness in demolishing of bacteria and microbes in medicine, for micro and macro algae. Our study was performed under laboratory conditions and was carried out in two main phases. In the first phase, spectral absorbance curves were established for micro and macro algae, the greatest absorbance value was determined in UV region (300 nm to 450 nm). In the second phase, to analyze the growth of algae species depending on UV-C illumination, micro algae within three different basins with the same cross-sectional area and different water depths (D1 :12.5 cm, D2:25 cm, D3:45cm) were exposed to UV-C radiation for different durations (2, 4, 6. 8 and 16 s). The maximum inhibition on the growth rate of A. maxima was observed in 16 s UV-C radiation treatment groups of D1 and D2 basins. Since Cladophora sp. macro algae are aquatic weeds floating over the water surface, they were exposed to UV-C radiation similar to micro algae only in D1 basin. The greatest reduction rate in biomass values of Cladophora sp. was observed in 16 s UV-C exposed groups.