The introduction and spread of non‐native species restructure native ecosystems and can be particularly impactful when invaders are ecosystem engineers or habitat‐forming species. In coastal, estuarine, and marine systems, submerged aquatic vegetation (SAV), like macroalgae and seagrasses, form key habitats for nekton, serving as nurseries, foraging grounds, and reproduction sites. If non‐native ecosystem engineers can provide sufficient structure and/or resources, they may exert a neutral or positive effect on organisms occupying higher trophic positions. As such, we hypothesized that nekton response to non‐native SAV species may be neutral or positive. We performed a quantitative meta‐analysis to quantify impacts of non‐native SAV on native crabs, fishes, and shrimps. We extracted data from 35 studies and evaluated 11 response metrics related to facilitation (e.g., habitat use and foraging), restricting our analysis to studies that compared at least one of these metrics in nekton from co‐occurring native and non‐native SAV habitats in marine, coastal, or estuarine systems. We found that nekton abundance, species richness, and biomass were the most assessed metrics of nekton performance. Our pooled data revealed differential results among response metrics, with nekton growth and reproduction enhanced in non‐native habitats and species richness enhanced in a native setting. The mean effect sizes for all other nekton response metrics, including abundance, had 95% CIs that overlapped zero, indicating no difference in response between native and non‐native SAV. For many endpoints, limited sample sizes prevented robust inferences, but they also highlighted areas where more research is needed in future studies. Non‐native species have the potential to restructure the systems they invade. Our results lend support to the relative trophic position hypothesis, indicating that non‐native habitat formers may facilitate native organisms in higher trophic levels. We identify research gaps that may guide future studies and allow for a more comprehensive understanding of responses to non‐native ecosystem engineers.