Various methods are available for monitoring pollution levels in surface water and sediments, including using organisms as bioindicators. Segara Anakan Lagoon is an estuarine ecosystem that could be affected by contaminants transported by rivers. Pollution sources include pesticides and fertilizers from upstream agricultural areas, domestic waste, and shipping traffic. Macrozoobenthos are among the organisms commonly used as bioindicators of environmental pollution. Macrozoobenthos live at the bottom of the water column, and as deposit feeders, they lend themselves to use as bioindicators. The structure of the macrozoobenthos community in Segara Anakan has changed, as evidenced by the diversity and abundance of benthic species. Furthermore, environmental pollution parameters, such as heavy metal concentrations in water and sediments, are relatively high in the lagoon. Concentrations of Hg, Pb, Cd, and Cr varied among collection sites, with average concentrations of 0.04, 4.4, 1.2, and 1.4 ppm, respectively. In general, the abundance of macrozoobenthos was low at collection stations with high heavy metal concentrations, demonstrating that heavy metal pollution has occurred in Segara Anakan. Correlation tests between macrozoobenthos and heavy metal concentrations in water and sediments yielded r-values of > 0.8225 and 0.7473, respectively.