Disturbances such as wildfire, insect outbreaks, and forest clearing, play an important role in regulating carbon, nitrogen, and hydrologic fluxes in terrestrial watersheds. Evaluating how watersheds respond to disturbance requires understanding mechanisms that interact over multiple spatial and temporal scales. Simulation modeling is a powerful tool for bridging these scales; however, model projections are limited by uncertainties in the initial state of plant carbon and nitrogen stores. Watershed models typically use one of two methods to initialize these stores: spin-up to steady state, or remote sensing with allometric relationships. Spin-up involves running a model until vegetation reaches equilibrium based on climate; this approach assumes that vegetation across the watershed has reached maturity and is of uniform age, which fails to account for landscape heterogeneity and non-steady state conditions. By contrast, remote sensing, can provide data for initializing such conditions. However, methods for assimilating remote sensing into model simulations can also be problematic. They often rely on empirical allometric relationships between a single vegetation variable and modeled carbon and nitrogen stores. Because allometric relationships are species- and region-specific, they do not account for the effects of local resource limitation, which can influence carbon allocation (to leaves, stems, roots, etc.). To address this problem, we developed a new initialization approach using the catchment-scale ecohydrologic model RHESSys. The new approach merges the mechanistic stability of spin-up with the spatial fidelity of remote sensing. It uses remote sensing to define spatially explicit targets for one, or several vegetation state variables, such as leaf area index, across a watershed. The model then simulates the growth of carbon and nitrogen stores until the defined targets are met for all locations. We evaluated this approach in a mixed pine-dominated watershed in central Idaho, and a chaparral-dominated watershed in southern California. In the pine-dominated watershed, model estimates of carbon, nitrogen, and water fluxes varied among methods, while the target-driven method increased correspondence between observed and modeled streamflow. In the chaparral watershed, where vegetation was more homogeneously aged, there were no major differences among methods. Thus, in heterogeneous, disturbance-prone watersheds, the target-driven approach shows potential for improving biogeochemical projections.