Community composition, species abundance, and species distribution are expected to change while monitoring ecosystems over time, and effective management of natural resources requires understanding mechanisms contributing to change. Marine ecosystems in particular can be difficult to monitor, in part due to large, multidimensional spatial scales and complex dynamics. However, within the temperate marine ecosystems, the nearshore food web is reasonably well described. This food web is ecologically and socially important, spatially constrained, and has been the focus of extensive experimental research that describes the underlying mechanisms important to system dynamics. Here, we describe a monitoring program initiated in 2006 that focuses on the nearshore benthic food web in the Gulf of Alaska, whose design anticipates potential causes of ecosystem change to improve rigor, resolution, and confidence in understanding the mechanisms underlying change. We established 15 long‐term monitoring sites across more than 1000 km of coastline, including 10 within two national parks and 5 within Prince William Sound, area of the 1989 Exxon Valdez oil spill. The program evaluates six ecological indicators and more than 200 species that range from primary producers to top‐level consumers, and is designed to examine both bottom‐up and top‐down dynamics. Employing a design that allows broad spatial inference and selecting species with direct food‐web linkages, we demonstrate the ability of our monitoring program to simultaneously detect change and assess potential mechanisms underlying that change. Detecting change and understanding mechanisms can help guide management and conservation policy. Specifically, we provide an example focusing on the sea otter (Enhydra lutris) that illustrates how (1) analytical methods are used to evaluate changes on various scales and infer potential mechanisms of change, (2) food‐web linkages can enhance the understanding of changes and their effects, and (3) data can be used to inform management.