The Long-Term Resource Monitoring element (LTRM) of the Upper Mississippi River Restoration program (UMRR) has conducted aquatic vegetation and water quality surveys in several navigation pools since the mid 1990’s. Over a 20-year period (1998-2017), the off-channel (i.e. backwater) areas in upper Pool 4 remained chronically turbid and supported a limited submersed macrophyte community with high between-year variability in the proportion of sites where submersed plants were observed. Water surface elevation and discharge rates also fluctuated substantially within- and between-years in the upper pool. Pearson correlation analysis indicated that between-year change in the proportion of sites where submersed macrophytes are observed is correlated to the number of high summer discharge days 1 year prior (r = -0.48); the number of low summer discharge days during the current year (r =0.46) and one year prior (r = 0.62); minimum discharge (r = 0.52) and the duration that depth at vegetation sample sites was within the estimated photic zone (i.e. a metric that reflects a combination of water clarity and water surface elevation) during the current summer (r = 0.63). Conditions more than one year prior and during the other seasons (winter, spring, fall) exhibited little correlation to subsequent fluctuations in the prevalence of submersed macrophytes.