The Boquerón Wildlife Refuge is the largest mangrove forest on Puerto Rico's west coast. Many of the mangrove channels there are periodically invaded by mats of the floating fern Salvinia. Since invasive plant species impact the biodiversity of wetlands, a monthly assessment of the aquatic macroinvertebrate diversity was conducted from June to November of 2013, in three mangrove areas invaded by Salvinia as well as three areas without it. Three sampling methods were used: aquatic light traps, emergence traps, and D-net sweeps. A total of 21,305 invertebrates representing 24 orders and 72 families were collected and identified. Diptera (21 families) showed the greatest taxonomic richness, followed by Coleoptera (12 families). Shannon-Weiner, Simpson, and Jaccard indexes were calculated per sampling method to compare the diversity between habitat-types. Permutational multivariate analysis of variance (PERMANOVA) indicated significant variations in abundances between habitat-types in light-traps and D-nets, while showing significant temporal variations in abundances in the emergence traps. Non-metric multidimensional scaling (NMDS) was used to represent the results of the PERMANOVA. Analysis of similarity (ANOSIM) and similarity percentage analysis (SIMPER) were employed to evaluate (dis-)similarities between habitat-types. Regardless of the type of trap, about half of the taxa were shared between the two habitat-types.