Abstract The output of organic pollutants and excessive nutrients in intensive agricultural areas has frequently occurred, which easily lead to pollution events such as harmful algal blooms in downstream aquatic ecosystems. A photobioreactor-wetland system was applied to remove UV 254 nm matter and dissolved nutrients discharged from an intensive agricultural area in the Kunming region of western China. The photobioreactor-wetland system was composed of two main components: an autotrophic photobioreactor with replanted macrophytes and a constructed wetland. The results showed that there was a significant correlation between UV 245 nm absorbance and chemical oxygen demand (COD) concentration in the effluent of the agricultural ecosystem. When the hydraulic load of the photobioreactor-wetland system was 500 m 3 day −1, the UV 254 nm absorbance was dramatically reduced, and dissolved nutrients such as TDP, NO 3–N and NH 4–N were effectively removed. The overall average removal efficiencies were as follows in relatively steady-state conditions: UV 254 nm matter (66%), TDP (71%), NO 3–N (75%) and NH 4–N (65%). Simpson's diversity index of zoobenthos indicated that the system could increase the zoobenthic diversity and improve the growth conditions of the zoobenthos habitat. The results also showed that the photobioreactor-wetland system could remove the UV 254 nm matter and dissolved nutrients, providing a promising bio-measure for reducing the risk of pollution event occurrences in downstream surface waters.