This report presents a broad overview of spatial and temporal variation in the water quality of the Upper Mississippi River System (UMRS). The Long Term Resource Monitoring Program (LTRMP) provides a systemic perspective through the collection and analysis of monitoring data from six study reaches representing the upper, lower, and open river reaches of the UMRS: Upper Mississippi River Pools 4, 8, 13, and 26 and Open River [near Cape Girardeau, Missouri]; and Illinois River. La Grange Pool. This report presents data from 1993 to 2001 (or 2002 when available) and focuses on spring and summer conditions. Water quality constituents (e.g., turbidity, suspended solids, chlorophyll, nutrients, and dissolved oxygen) varied among study reaches, aquatic area (e.g., main channel, contiguous backwaters, etc.) and seasons. For example, turbidity and suspended solids varied substantially among pools. Turbidity and suspended solids were much lower in lower Pool 4 than in upper Pool 4 because of the trapping of sediments by Lake Pepin, but increased in each of the study reaches from Pool 4 to Open River. Chlorophyll a and nutrient concentrations often differed between the main channel and contiguous backwater areas (hereafter referred to as backwaters). Summer chlorophyll a concentrations were generally higher in backwaters than in the main channel, and summer nitrate + nitrite (NOx) concentrations were generally lower in backwaters than in the main channel. Seasonal patterns were evident in chlorophyll a, nutrient, and dissolved oxygen concentrations. Main channel soluble reactive phosphorus concentrations peaked in September and exhibited minima in April and May. In contrast, main channel and backwater NOx concentrations exhibited minima in fall when soluble reactive phosphorus concentrations are at their maximum. Seasonal chlorophyll a concentrations in main channels and backwaters show peaks in late summer and fall, with minima in winter and early summer. Seasonal dissolved oxygen patterns differed slightly among the northern (Pools 4, 8, and 13) and southern (Pool 26, Open River, La Grange Pool) study reaches. In the northern study reaches, dissolved oxygen concentrations are generally highest in spring, lowest in summer and winter, and intermediate in fall. In the southern study reaches, dissolved oxygen concentrations are highest in winter, lowest in summer, and intermediate in spring and fall. Spatial patterns within study reaches caused by tributary inputs were shown by the spatial patterns in specific conductivity. Of the six LTRMP study reaches, Pools 4, 8, and 26 showed clear spatial patterns in conductivity related to tributary input in some years whereas Pool 13, Open River, and La Grange Pool did not.