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The potential for animals to modify spatial patterns of nutrient limitation for autotrophs and habitat availability for other members of their communities is increasingly recognized. However, net trophic effects of consumers acting as ecosystem engineers remain poorly known. The American Alligator Alligator mississippiensis is an abundant predator capable of dramatic modifications of physical habitat through the creation and maintenance of pond-like basins, but its role in influencing community structure and nutrient dynamics is less appreciated. We investigated if alligators engineer differences in nutrient availability and changes to community structure by their creation of 'alligator ponds' compared to the surrounding phosphorus (P)-limited oligotrophic marsh. We used a halo sampling design of three distinct habitats extending outward from 10 active alligator ponds across a hydrological gradient in the Everglades, USA. We performed nutrient analysis on basal food-web resources and quantitative community analyses, and stoichiometric analyses on plants and animals. Our findings demonstrate that alligators act as ecosystem engineers and enhance food-web heterogeneity by increasing nutrient availability, manipulating physical structure and altering algal, plant and animal communities. Flocculent detritus, an unconsolidated layer of particulate organic matter and soil, showed strong patterns of P enrichment in ponds. Higher P availability in alligator ponds also resulted in bottom-up trophic transfer of nutrients as evidenced by higher growth rates (lower N:P) for plants and aquatic consumers. Edge habitats surrounding alligator ponds contained the most diverse communities of invertebrates and plants, but low total abundance of fishes, likely driven by high densities of emergent macrophytes. Pond communities exhibited higher abundance of fish compared to edge habitat and were dominated by compositions of small invertebrates that track high nutrient availability in the water column. Marshes contained high numbers of animals that are closely tied to periphyton mats, which were absent from other habitats. Alligator-engineered habitats are ecologically important by providing nutrient-enriched 'hotspots' in an oligotrophic system, habitat heterogeneity to marshes, and refuges for other fauna during seasonal disturbances. This work adds to growing evidence that efforts to model community dynamics should routinely consider animal-mediated bottom-up processes like ecosystem engineering., (© 2023 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)