This study was carried out in the Souris and Turtle Rivers in North Dakota. The aim of this study was to develop multi-element fingerprints of the Souris River and Turtle River sediments and to evaluate the suitability of these fingerprints to assess the geographic origin of potential pollutants of the two rivers. Preliminary analysis of Souris River sediment samples confirmed that the multi-element fingerprinting can be used to assess the sediment and contaminant loading patterns. Laboratory experiments were performed to assess the validity of linear mixing assumption in multi-element fingerprinting studies. The results of these experiments verified the assumptions and showed that there is a statistically significant spatial and temporal variation in the element concentrations depending on their mobility and re-deposition. Field studies were conducted in the Souris River and Turtle River to assess the variation of element concentrations in the top riverbed samples along the main rivers and their tributaries. The sediment contribution from the tributaries and the phosphorus concentrations in the main channel were used to calculate the phosphorus contributions from the tributary sediments to the Souris River. The differences in phosphorus contributions from tributaries were related to land use, underlying geology, and the size of the watersheds of the tributaries in the Souris River watershed. Similar analysis was used in the Turtle River to calculate Arsenic, Cadmium and Selenium contribution from the tributaries to the Turtle River. The differences in the contribution of these elements were related to the underlying geology and the size of the watersheds. This study provides a detailed analysis of element concentrations and relative sediments and element loading rates from the tributaries to the main rivers along the Souris and Turtle Rivers in North Dakota. The multi-element fingerprinting technique can be successfully used as a tool to identify the relative contribution of sediments and assessing and tracing pollution sources in rivers. Multi-element fingerprinting provides a relatively low cost, rapid tool for sediment tracking, without the need for addition of exotic chemicals such radio-tracers or dyes to natural ecosystems.