The rivers in the Hungarian Upper Tisza Region are frequently polluted mainly due to mining activities in the catchment area. At the beginning of 2000, two major mining accidents occurred in the Romanian part of the catchment area due to the failure of a tailings dam releasing huge amounts of cyanide and heavy metals to the rivers. Surface sediment as well as water samples were collected at six sites in the years 2000–2003, from the northeast-Hungarian section of the Tisza, Szamos and Túr rivers. The sediment pollution of the rivers was compared based on measurements of bulk material and selected single particles, in order to relate the observed compositions and chemical states of metals to the possible sources and weathering of pollution. Non-destructive X-ray analytical methods were applied in order to obtain different kinds of information from the same samples or particles. In order to identify the pollution sources, their magnitude and fate, complementary analyses were carried out. Heterogeneous particulate samples were analyzed from a large geographical territory and a 4-year time period. Individual particles were analyzed only from the “hot” samples that showed elevated concentrations of heavy metals. Particles that were classified as anthropogenic were finally analyzed to identify trace concentrations and chemical states of heavy metals. Although the Tisza river was affected by water pollution due to the two major mining accidents at the beginning of 2000, the concentration of heavy metals in sediments decreased to the mineral background level 1 year after the pollution event. In the tributaries Szamos and Túr, however, no significant decrease of the heavy metal concentrations was observed in the recent years, indicating a continuous pollution. Among the water suspended particles collected from river Túr, fibers of unknown origin were observed by electron microscopy; these particles were aluminosilicates enriched in Zn and Mn. Cd was also concentrated in this particle type. Zn in the sulfide form was observed by microbeam X-ray absorption near-edge structure analysis only in the samples collected from river Tisza in 2000, while this metal was connected to carbonates and silicates in the other samples. The dissolved Zn content of the river water and the chemical state of Zn in the fibers collected from river Túr indicate that the heavy metal pollution arrived to the Hungarian section originally mostly in the dissolved phase. The accidental heavy metal pollution of River Tisza, however, was in the form of microscopic metal sulfide particles.