© The Editor(s) if applicable and the Author(s) 2016. This study investigates the source and flux of particulate 129I in the downstream reaches of the Niida River system in Fukushima. The upper watershed is a relatively highly contaminated zone located 30–40 km northwest of the Fukushima Daiichi Nuclear Power Plant. Samples of total suspended substance (SS) were collected continuously at Haramachi (5.5 km upstream from the river mouth) from December 2012 to January 2014 using a time-integrative SS sampler. Activity of 129I and the 129I/127I ratio in SS were 0.9–4.1 mBq kg−1 and (2.5–4.4) × 10−8, respectively, and were strongly correlated with the total dry weight of SS samples with R2 of 0.79–0.88. High SS 129I activity and 129I/127I ratios were found in March, April, September, and October 2013. SS 129I activity and 129I/127I ratios are considered to reflect the SS source, i.e., the more contaminated upper watershed or the less contaminated downstream area. The flux of particulate 129I at the Haramachi site was estimated to be 7.6–9.0 kBq month−1 during September–October 2013. A relatively high amount of particulate 129I may have been transported from the upstream to the downstream reaches of the Niida River by high rainfall over this period.