Citarum River is the longest and largest river in West Java, and its existence greatly influences the lives of surrounding communities. Many industries are built around the area. It is important to assess the quality of the water, because certain heavy metal might leak to the body of water. This research aimed to investigate the mitotic index (MI), root length, frequency and types of chromosomal aberration which determined the cytotoxicity and genotoxicity by using Allium cepa L. as biomarker. The Completely randomized design with seven treatments and four replications were used. Observation was done 96 hours after onion bulb soaked in water. Data was analysed using Analysis of Variance and continued with Duncan post-hoc. Results showed that root length was not affected. Water samples were affecting the MI, frequency, and types of chromosomal aberration. The highest number of chromosome aberrations was recorded on Dayeuh Kolot stations and the most common type of aberration was stickiness. The chromosome aberrations observed were; stickiness, chromosome loss, chromosome bridge, chromosome break, binucleated cells, multipolar, micronuclei, and c-mitosis. Based on the results, Allium assay is beneficial to evaluate the level of cytotoxicity and genotoxicity in the upstream Citarum River.