Freshwater ecosystems are critical zones of nutrient and carbon (C) processing along the land-sea continuum. Relative to our understanding of C, nitrogen (N), and phosphorus (P) cycling within the freshwater systems, the controls on silicon (Si) cycling and export are less understood. Understanding Si biogeochemistry and its coupled biogeochemical processing with N and P has direct implications for both freshwater and coastal ecosystems, as the amount of Si in relation to N and P exported by rivers to coastal receiving waters can determine phytoplankton species assemblages, which in turn affects C cycling and food web structure. Here we examine the relationships between dissolved Si (DSi), total nitrogen (TN), and total phosphorus (TP) concentrations, and how these relationships relate to basin land cover, lithology, and river hydrogeomorphology (i.e., among different ‘aquatic areas’) in the Upper Mississippi River System (UMRS) using two datasets (one from the tributaries and one from the mainstem) that span a nine-year period (2010-2018) representing >10,000 unique samples. We found significant declines in DSi concentrations, as well as Si:TP and Si:TN ratios along the north-south gradient of the mainstem UMRS across all six aquatic area types. This signal was driven partially by a corresponding decline in tributary DSi inputs along this latitudinal gradient. Contrary to findings from other regions of North America, basin land cover was not an important predictor of tributary DSi concentrations, especially compared to lithology. However, Si:TN and Si:TP ratios appear to be strongly controlled by basin land cover, likely due to excess N and P loading from row-crop agriculture. Si, and its ratio with N and P (i.e., Si stoichiometry), was similar across most aquatic area types, including run-of-river impoundments and the main channel, suggesting similar processes affecting Si, N, and P concentrations in these reaches. However, backwater lakes had lower DSi and TN concentrations and compared to the other aquatic area types, highlighting the importance of water residence time and nutrient uptake in controlling Si stoichiometry in inland waters. Together, our results show rivers are not simple pipes for Si, but rather the complexity in watershed characteristics, hydrology, and biological uptake results in dynamic Si stoichiometry along the river continuum.