The colonization and spread of non-native species are recognized as a critical driver of environmental change in mangrove ecosystems. However, environmental factors that favor non-native plant colonization in mangroves are still poorly understood. To contribute to filling this gap, we investigated the effect of selected abiotic factors associated controlling aquatic macrophytes colonization in mangroves in Southeastern Brazil. Furthermore, we also assessed foliar attributes of native and non-native species to evaluate whether biotic attributes favored the colonization. We selected 18 plots in mangrove forests under different levels of anthropogenic N inputs, both colonized and non-colonized by aquatic macrophytes in the Estuarine-Lagoon Complex of Cananeia-Iguape, southeastern Brazil. We measured interstitial salinity, sediment nitrate and ammonium concentrations, and sediment physicochemical properties. We also measured foliar nitrogen (N) concentrations, foliar C:N, and foliar δ13C of both native and non-native species. We found that interstitial salinity at 10 cm depth followed by nitrate concentrations in sediment were the main factors associated with the occurrence of aquatic macrophytes in the studied mangrove areas. Moreover, non-native species had about 2-fold higher foliar N concentrations as well as about a 1.5-fold lower C:N ratios compared to native species. Low salinity and increased N availability in sediment allowed for the success of aquatic macrophytes into mangrove forests, also resulting in high amount of dead mangrove trunks (up 53% of basal area).