Classic bottom-up theory predicts that increased resource availability (for example, nutrients) at the base of the food web will stimulate primary production and, in turn, secondary production. Recent studies, however, indicate that bottom-up controls on food web production can be modified by other factors, such as landscape configuration and continuity. As part of a 10-year ecosystem-scale experiment in a New England salt marsh, we investigated the response of secondary consumers, specifically a fish, the mummichog (Fundulus heteroclitus), to nutrient enrichment. In the first 6 years, we observed a classic bottom-up response of increased production of algae, invertebrate prey, and mummichogs. After the sixth year, however, mummichog biomass declined to below reference levels by the eighth year. This decline in mummichog biomass coincided with nutrient-induced collapse of the low-marsh habitat. Based on stable isotope analyses, field surveys, and small-scale experiments, we suggest that the geomorphic changes induced a trophic decoupling between creek and marsh habitats, thereby reducing mummichog access to prey in the intermittently flooded marsh. Thus, despite continued stimulation of algal and invertebrate prey production, fish abundances declined to below pre-enrichment levels. Our results demonstrate how geomorphic controls can override classic bottom-up control and emphasize the importance of long-term studies in detecting the response of slow-turnover phenomena (for example, changing landscapes).