System-scale restoration efforts within the Upper Mississippi River Restoration Program have included annual monitoring of submersed aquatic vegetation (SAV) since 1998 in four representative reaches spanning approximately 440 river km. We developed predictive models relating monitoring data (site-scale SAV abundance indices) to diver-harvested SAV biomass, used the models to back-estimate annual standing stock biomass between 1998 and 2018 and compared biomass estimates to previous abundance measures. Two morphologically distinct groups of SAV with differing sampling efficiencies were modeled and estimated separately: the first category included only Vallisneria americana which has long, unbranched leaves and dominates lotic environments, while the second category included 17 branched morphology species (e.g. Ceratophyllum demersum and Elodea canadensis) that dominate lentic environments. Two non-native species (Myriophyllum spicatum and Potamogeton crispus) were included in the branched category for model development but were estimated separately as a fraction of branched species biomass due to a small sample size and a lack of training data.