The global degradation of wetlands is increasing their susceptibility to invasions, which is greatly determined by a niche overlap between native and invasive species. We analyze its role in regulating the coexistence of the native Mediterranean stripe-necked terrapin Mauremys leprosa and the invasive Red-eared Slider Trachemys scripta elegans in a coastal wetland. We analyzed both water chemistry and landscape attributes, using variance-partitioning analysis to isolate the variance explained by each set of variables. Then, the influence of environmental variables on species co-occurrence patterns was assessed by using latent variable models (LVM), which account for correlation between species that may be attributable to biotic interactions or missing environmental covariates. The species showed a very low niche overlap, with clear differences in their response to environmental and landscape filters. The distribution of T. s. elegans was largely explained by landscape variables, preferring uniform landscapes within the daily movement buffer, whereas at larger scales, it was associated with a high diversity of habitats of small and uniform relative sizes. A high percentage of the distribution of M. leprosa was unexplained by the measured variables and may be related to the competitive exclusion processes with T. s. elegans. The species was positively related with large patches with high perimeter values or ecotone area at medium spatial scales, and it was benefited from a marked heterogeneity in the patches’ size at larger scale. According to latent variable models, both species had wide eutrophication and salinity tolerance ranges, but they showed different environmental preferences. T. s. elegans was related to eutrophic freshwater environments, whereas M. leprosa was related to more saline and less eutrophic waters. Our results suggest that M. leprosa modifies its habitat use in order to avoid interaction with the T. s. elegans. Thus, management actions aimed at removing the invasive species from the territory and promoting habitat heterogeneity might be needed to protect M. leprosa and avoid local extinctions.