Distribution and frequency of submersed aquatic vegetation in the Upper Mississippi River System are monitored as part of the Long Term Resource Monitoring Program. This report summarizes results of sampling aquatic vegetation along fixed transects in Navigation Pools 4, 8, 13, and 26 in the Upper Mississippi River and La Grange Pool in the Illinois River in 1996. Plants were sampled at regular intervals along fixed transects using a modified rake technique. Sampling was conducted twice during the growing season (spring and summer). Twenty-four submersed and rooted floating-leaved species were found. Most species were found in Pools 4, 8, and 13. Pool 26 had the fewest (3) number of species and Pool 4 had the greatest (23), including most large-leaved pondweeds and the first LTRMP record of floating pondweed (Potamogeton natans). Sago pondweed (P. pectinatus) and coontail (Ceratophyllum demersum) were dominant in the contiguous backwaters sampled. Seasonal trends were observed in nine species, all of which, except sago pondweed, increased later in the season. Throughout the growing season, more sites were vegetated in Pools 8 and 13 and La Grange Pool (frequency of 50 73%) than in Pools 4 and 26 (<25%). Pool 26 was devoid of vegetation during the second sampling. Aquatic vegetation was generally rare in contiguous areas of Pool 26 and La Grange Pool, but more plentiful in the isolated, managed backwaters of La Grange Pool.