Invasive aquatic weeds negatively affect biodiversity, fluvial dynamics, water quality, and water storage and conveyance for a variety of human resource demands. In California's Sacramento-San Joaquin River Delta, one submersed species Brazilian egeria-and one floating species-water hyacinth-are actively managed to maintain navigable waterways. We monitored the spatial and temporal dynamics of these species and their communities in the Sacramento-San Joaquin River Delta using airborne hyperspectral data and assessed the effect of herbicide treatments used to manage these species from 2003 to 2007. Each year, submersed aquatic plant species occupied about 12% of the surface area of the Delta in early summer and floating invasive plant species occupied 2 to 3%. Since 2003, the coverage of submersed aquatic plants expanded about 500 ha, whereas the coverage of water hyacinth was reduced. Although local treatments have reduced the coverage of submersed aquatic plants, Delta-wide cover has not been significantly reduced. Locally, multiyear treatments could decrease submersed aquatic plants spread, given that no residual plants outside the treated area were present. In contrast, the spread of water hyacinth either has been constant or has decreased over time. These results show that (1) the objectives of the Egeria densa Control Program (EDCP) have been hindered until 2007 by restrictions imposed on the timing of herbicide applications; (2) submersed aquatic plants appeared to function as ecosystem engineers by enabling spread to adjacent areas typically subject to scouring action; (3) repeated herbicide treatment of water hyacinth has resulted in control of the spread of this species, which also appears to have facilitated the spread of water primrose and floating pennywort. These results suggest that management of the Delta aquatic macrophytes may benefit by an ecosystem-level implementation of an Integrated Delta Vegetation Management and Monitoring Program, rather than targeting only two problematic species.