AbstractThe effects of long‐term experimental nutrient enrichment on nematode trophic guilds and morphometrics were examined in intertidal saltmarsh creeks of Plum Island Estuary, Massachusetts, USA. Nematodes from the marsh‐edge Spartina alterniflora habitat in a reference creek (n = 3300) were sampled annually and compared with nematodes (n = 3100) from a creek in which nitrate and phosphate loading rates were increased approximately 10–15× for 6 years. Trophic guilds in both creeks were dominated by epistrate (diatom) feeders and predators, and natural temporal variability across years was high. However, after 4 years of nutrient enrichment, a shift in the nutrient‐enriched creek was detected from a dominance of epistrate feeders to an increased proportion of predators, even though neither the benthic microalgae biomass nor the total density of nematodes was affected by fertilization. Nematodes also became longer, and longer relative to their diameter over time with nutrient enrichment because of the shift in trophic structure as short‐stout epistrate feeders were replaced with longer, more slender predators. These changes may have been directly related to nutrient enrichment effects on benthic algae or indirectly to the many other effects of enrichments on ecosystem structure or function. Our research indicates that nutrient enrichment alters the nematode community and this alternation may directly or indirectly affect the response of benthic algae to nutrient enrichment and as well as other ecosystem services.