Urban forests are repeatedly characterized as distinct in composition and structure in comparison with their non-urban counterparts. This holds true for mangroves, although previous studies lack quantified representations of urbanness as well as any inclusion of hydrology or water chemistry, which are important influences on mangrove forest structure, composition, and function. This study uses LiDAR and ground-based measurements of mangroves within well quantified urban gradients in Puerto Rico to test for the relative importance of urbanization alongside flooding metrics and surface water chemistry in explaining observed patterns of forest structure and composition. In simple regression, urban metrics were the most powerful predictors of forest composition but not structure. Results show higher tree diversity but lower mangrove diversity in the most urban forests. Structural measurements, however, were best explained by flooding, surface water chemistry, and non-urban land cover metrics. Nitrogen concentrations best explained stem density and tree size, while flooding metrics best explained stand biomass and basal area, and surrounding vegetation cover best explained canopy cover and height metrics. In multiple regression, land cover and surface water chemistry were more important than flooding, with population density again being the most important variable in explaining mangrove forest diversity. Results show that urbanization is an important influence on mangrove composition and basal area, leading to higher tree diversity and lower basal area, consistent with patterns in terrestrial forests. But urban mangrove forests are also lower in mangrove diversity and tend to have representation only by Laguncularia racemosa. Nitrogen concentrations and surrounding vegetation cover, both of which are indirectly influenced by urbanization, were positively related to tree size and canopy cover and height, respectively. These tests suggest urbanization is an important influence on mangrove forest structure and composition, but that flooding and water chemistry must also be considered when managing these forests.