The National Ecological Observatory Network (NEON) is a continental-scale observatory facility that provides long-term, open-access ecological data from 81 field sites across the United States, including Alaska, Hawaii, and Puerto Rico. NEON's objective is to provide the scientific community with free, high-quality data that can be used to understand the drivers of and response to environmental changes in ecosystems across the United States. For this, NEON is involved in an initiative aimed at equipping researchers with the necessary data and tools to enhance their understanding of aquatic ecosystems throughout the United States. Currently, NEON employs a massive systematic sampling design that collects over 180 types of data, including metabarcoding, at varying spatial and temporal scales. The metabarcoding data allows the scientific community to analyze the biodiversity and biomonitoring in different environments at different scales. In this research, we utilized NEON's macroinvertebrates metabarcoding sampling data to assess the diversity of macroinvertebrates within two wadeable streams sites in Puerto Rico. The macroinvertebrate’s sampling is collected once a year during peak production in summer at Rio Yahuecas (GUIL) and Rio Cupeyes (CUPE). These two sites differ in characteristics; Rio Cupeyes is located in the Center-Southwest of Puerto Rico and is characterized by dense forest riparian. In contrast, the Rio Guilarte site is located in the mountains of Puerto Rico and is affected by agricultural runoff in the watershed. Samples were collected using a Surber sampler in three riffles across the NEON 1-kilometer reach. Sample was collected using aseptic tactics to prevent contamination, preserved in 95% ethanol and ethanol change withing 24 hours. Samples were shipped to an external laboratory for DNA extraction and sequencing. A comparison of the macroinvertebrate community composition between these two sites reveals significant differences.