Aquatic vegetation of the Upper Mississippi River System is monitored as part of the Long Term Resource Monitoring Program. This report summarizes the 1994 effort of monitoring submersed aquatic vegetation (SAV) along transects permanently established in vegetated locations within four navigation pools of the Upper Mississippi River and one navigation pool of the Illinois River. A total of 17 species of SAV were found along transects during the 1994 season. Several additional species were found during informal surveys. More species of submersed aquatic macrophytes were found along transects in lower Pool 4 than in any other reach. Across all pools, sago pondweed (Potamogeton pectinatus) was the species most frequently found. Several species of SAV were seasonally dynamic at the transect locations, with changes in frequencies especially common among sago pondweed and curly pondweeds (P. crispus). The proportion of sites with SAV decreased significantly in Pool 4, increased in Pool 13, but did not change within other pools. Pool 26, however, was not sampled during the summer sampling season because the transect locations were dewatered to promote growth of annual plant species. Mean depths of sites with SAV ranged from 0.4 m in Pool 26 during spring sampling to 1.5 m in La Grange Pool during spring and summer sampling.