As human populations increase in watersheds, the Peconic Bay estuary (NY) has experienced increased nitrogen (N) loads, resulting in eutrophication. Stable isotopes can be used as indicators of anthropogenic N sources such as wastewater and fertilizer, and potentially be used to track source-specific N inputs through time. We hypothesized that Peconic Bay scallops (Argopecten irridians) could be proxies for these environmental changes through assimilation of organic matter from surrounding water into their soft tissue and shells. We examined nitrogen stable isotopes (δ15N) from whole soft tissue and shell of scallops collected throughout the Peconic. A strong correlation was found between shell and soft tissue δ15N values, suggesting that scallop shells are reliable proxies for soft tissue. Scallops from sites with higher percentages of N from wastewater had enriched δ15N values, whereas sites with higher percentages of fertilizer N inputs had depleted δ15N values in scallop shells and tissues. Thus, no significant relationship was found among sites between total watershed N yield and shell or soft tissue δ15N. This study is among the first to demonstrate fertilizer-derived N being incorporated into bivalve shell, which has implications for tracking long-term fertilizer inputs to watersheds on an annual time scale using archival shells.