The upper Malwathu Oya is a seasonal river. The main livelihood of people living in the immediate vicinity of the river is paddy cultivation, and chronic kidney disease is reported among them. Farmers utilize different types of agricultural chemicals in their fields expecting bumper harvests. Several agricultural chemicals have been reported to contain toxic trace elements in Sri Lanka. Therefore, arsenic and cadmium might end up in the river water. The presence of these trace elements in the river water and sediments can result in their bioaccumulation in fish tissues. The main purpose of this study was to investigate the presence of two trace elements in water and sediments, as well as in fish tissues (gills, kidney, liver and muscle) of three food fish species, Etroplus suratensis, Anabas testudineus and Channa striata during cultivating and non-cultivating seasons of the year. Further, the level of bioaccumulation of two trace elements in fish tissues in relation to the contamination level of water and sediments was assessed. Data were gathered for 43 months. Arsenic and cadmium concentration in water showed a significant (P < 0.05) seasonal variation. Generally, the two trace elements in the river water were highest during the cultivating seasons than in other seasons. In all species, both trace elements in the gills highly depended on the concentration in the water. In all species, two trace elements in water and sediment did not significantly affect the levels in muscle tissue. Therefore, the trace element levels in the edible parts of these three fish were well below the maximum permissible levels of international institutions.