We assessed the effects of local environment on survival, growth, and development in six clones (genotypes) of Vallisneria americana grown at five sites in the Huron-Erie Corridor. Detrimental effects of local environment on plant performance (rate of clonal growth, leaf and root production, surface area of leaves and roots, plant biomass, rate of flowering, and turion production) were correlated with sediment toxicity and levels of organic contamination determined in independent studies, and differed among plant genotypes. All surviving clones used in the study ranked environmental quality of the five sites in the same order. Two genotypes, which were tolerant of contaminants, survived the 2 yr of exposure at all sites, while other nontolerant clones died within the 1st yr of study, at the two most contaminated sites. The leaf-to-root surface area ratio was highly indicative of site quality, and was not affected either by year-to-year variation, or by differences between genotypes. The use of cloned plants in this biomonitoring study reduced variance, and increased precision and accuracy of site assessment compared to biomonitoring with genetically variable plants. Clones of V. americana tolerant of contaminants were particularly useful in assessing the most contaminated sites. An approach that uses an array of both tolerant and nontolerant clones is recommended.