Aquatic macroinvertebrates were used as bioindicators to determine the water quality of the river through the calculation of the Puerto Rico Biological Monitoring Working Party (BMWP-PR) and its degree of contamination with the Puerto Rico-Family Biotic Index (FBI-PR). Bimonthly sampling events from four sampling sites were made for a period of 12 months. Sampling sites were positioned upstream and downstream within the nature reserve, and outside and downstream the limits of the nature reserve. Results showed that the site upstream–inside the nature reserve had good water quality, and the site downstream–inside the nature reserve had regular water quality. Water quality outside-downstream the nature reserve was poor. There was mild organic contamination inside the nature reserve, while there was substantial organic contamination in the site that was outside-downstream the nature reserve. We concluded that the section of the river located within the nature reserve had a better ecological condition than the stretch of the river located outside-downstream of the nature reserve because it is located within a protected area that has been barely impacted by human activity.