The inflow of transuranium elements to the Yenisei River was previously associated with the production of weapons-grade plutonium at the Mining-and-Chemical Combine (MCC, Zheleznogorsk, Russia), but the source of transuranium elements in the River today is fabrication of MOX fuel that started recently at the MCC. The current study presents results of sequential chemical extraction of radionuclides from sediment samples collected in 2014 and 2020 in two areas near the MCC discharge site and compares these results with the data obtained previously by sequential extraction of sediments collected during 1999–2007. Over the study period, the strength of binding of 137Cs and 60Co in the Yenisei River sediments was high (up to 100%) and remained so, while the percentages of 241Am and 152Eu in residual solids after sequential extraction increased considerably and the percentage of 239,240Pu in residual solids decreased in samples from all study areas. In samples collected at the position located close to the MCC discharge site, the percentages of the strongly bound 241Am and 152Eu as well as 239,240Pu were lower than in the samples from the other positions. The study demonstrated an enormous increase in 239,240Pu activity concentration in the top sediment layers collected at all positions in 2020 relative to 2014. In the same period, as literature data suggest, 239,240Pu activity concentrations also increased in aquatic organisms of the Yenisei River, which can be indicative of the growing potential bioavailability of plutonium in the aquatic ecosystem, which could be caused by the presence of the mobile form of plutonium in the routine discharges from the MCC.