The restoration of chemically degraded rivers, lakes, and estuaries with large watersheds and pollution sources that are primarily diffuse in nature requires the grading of thousands of kilometers of tributary streams. Many population-and community-oriented biomonitoring methods have been developed that avoid the cost limitations of chemical/biomarker/bioassay approaches and the serious limitations of single-factor analysis as related to complex systems. In this study of the coastal plain and piedmont geomorphologic provinces of the Chesapeake Bay watershed, we have demonstrated a set of quantitative measures based on analysis of macrophyte populations that provide statistically significant separation of streams in accordance with their state-issued water quality rating. Macrophytes can be abundant and diverse in lower-order streams, and they demonstrate patterns of community structure and diversity similar to those of other organisms developed for biomonitoring of stream degradation. Unlike organisms previously and extensively used in biomonitoring techniques, however, macrophytes are considerably easier to identify and quantify. In addition, macrophyte techniques provide a range of measures of increasing sensitivity from species numbers at a few sites, to the presence/absence and abundance of indicator species, and, finally, to a diversity analysis based on easily identified species at an extended number of sites. We suggest that the ease of utilization of this methodology will allow repeated surveys of all streams in large watersheds with the invertebrate, fish and diatom biomonitoring to biomarking and chemical bioassays and finally analytical chemistry, progressively applied to verify and then identify specific pollution sources (“hot spots”) in a more limited number of problem streams.