Due to the sensitivity of invertebrates to environmental changes, their presence can serve as an indicator of coral reef health and water quality. This study seeks to ascertain the abundance of invertebrates, the structure of the invertebrate community, and their relationship with coral cover and water quality parameters in the waters of Sempu Strait. The belt transect method and the underwater photo transect (UPT) are used to determine the abundance of invertebrates and coral cover, respectively. Temperature, pH, DO, salinity, and water clarity are measured for water quality. According to the study's findings, seven of the nine invertebrate species were found. Between October 2021 and May 2022, seven of nine invertebrate biota categories, 733 species, and 606 species dominated by Diadema sea urchins were observed every two months. The invertebrate abundance ranged from 0.024 to 0.512. A low and imbalanced invertebrate diversity ranges from 0.078 to 0.493 (H' < 1). The range of the equality index (E < 0.4) is between 0.04 and 0.22, indicating a low community index. There are three levels of dominance index values: low, medium, and high. Due to their abundance, Diadema sea urchins dominate the Sempu Strait, particularly near the Jetty Station with its port activity. Coverage of coral reefs varies between 6% and 21.3%, indicating low and damaged corals. The correlation between coral cover and invertebrate abundance is moderate in Banyu Tawar and Rumah Apung (0.480 to 0.490), whereas it is weak in Waru-Waru, Watu Meja, and Jetty (-0.037-0.225). The abundance of invertebrates has a weak link with values ranging from -0.037 to -0.283 for water clarity, temperature, salinity, DO, and pH, but it has a strong correlation with a value of 0.610 for current velocity. The environment, including human activities and water quality, has a significant impact on macroinvertebrate communities. Environmentally tolerant macroinvertebrates will outcompete the vulnerable ones.