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Living shorelines, a prevalent nature-based coastal infrastructure technique, typically merge the restoration of coastal habitats (e.g., salt marsh, oyster reef) with gray infrastructure (e.g., rock or concrete breakwaters) to provide coastal erosion protection. With increasingly frequent and severe storms, living shorelines have been shown to effectively limit coastal erosion and loss; however, there is still uncertainty regarding the effects of living shorelines on nekton communities as compared to natural marshes and gray coastal protection strategies like bulkheads. Here, we present a dataset of living shoreline-associated nekton species recorded over a 20-year period in North Carolina, USA. We harmonized nekton abundance and biomass data from five different studies (each ranging in duration from 2 to 4 years) across 12 living shorelines with paired natural marshes and, in some cases, bulkheads. These studies used different gear types and sampling methodologies, and therefore future users of this dataset must carefully consider the limitations of different subsets of the data and ensure that they do not make direct catch comparisons across sites that used different methodologies. Altogether, we identified a total of 62 species groups at living shorelines, natural reference marshes, and bulkheads across three categories (i.e., crustacean, mollusk, and fish) between 2001 and 2024. We identified 49 species groups on living shorelines, 49 species groups in natural marshes, and 5 species groups on bulkheads. For each living shoreline and paired natural marsh and/or bulkhead shoreline, we report individual species counts, biomass (when available), and the sampling method. In addition, we report on the living shoreline type, age, and location. In total, these data provide vital insight into how living shorelines function as habitat for nekton, and they can be used to evaluate living shoreline effectiveness as a predominant nature-based solution for coastal protection and biodiversity enhancement. The data are released under the Creative Commons Attribution 4.0 International License.