The macrozoobenthic structure inhabiting marine ecosystem may be used as a bioindicator of changes in aquatic environmental disturbance. This study is aimed to assess environmental disturbance by application of biomonitoring using macrozoobenthic assemblages at coastal area of Menjangan Besar Island, Kepulauan Karimunjawa, Indonesia. The macrozoobenthic assemblages were assessed at two sampling locations, i.e. floating net cage of monoculture and reference areas. Each sampling location consisted of three stations with three replicates for each station. The samples were taken in two sampling times, i.e. August and November 2018. Data of abiotic parameters included the composition of organic matter content, sediment substrates, DO, pH, salinity, temperature, and water current. Sediments were sampled using Ekman grab from 15 m deep. The relationship between biotics (macrozoobenthos) and abiotics (physical-chemical factors) was assessed using a non-parametric multivariate procedure (BIO-ENV; Primer 6.1.5). Macrobenthic assemblages consisted of 89 species with the total abundance of 50,071 individuals/m2, consisting of 52 families and 4 classes of macrozoobenthos. The values of indices were ranging from 2,54-3,40 for diversity index (H'), 0,99 for Pielou’s evenness index (e’), and 0,09-0,17 for dominance index (C). The most common classes were a member of Gastropods and bivalves. Diversity and evennes indices exhibited differed by location (monoculture vs reference) and time sampling. Fluctuation of macrobenthic structure was considered as a results of environmental changes spatially and temporally, especially sediment composition and food availability as the form of organic matter. Nitrogen and silt were the most chemical and physical factors influencing the structure of macrozoobenthos (r = 0,632; BIO-ENV).