Estuary and river mouth are essential habitats for many commercial estuarine fishes, including the Sciaenidae family. While recently, estuaries have been threatened by anthropogenic marine litter (AML) transported from nearby land and river. An important type of AML is plastic litter since it takes a long degradation time. In the South Sumatra Province, Indonesia, one of the vital estuaries is the Musi estuary. This paper aims to map the spatial distributions of two Sciaenids, including Panna microdon and Otolithoides pama, and Sciaenid’s environmental covariates, including water quality, chlorophyll a, and plastic litters in Musi estuary and model the correlations of Sciaenids with their covariates. The maps were developed using GIS, and the model was validated using AIC methods. The data were collected from 3 river mouths in the west, central, and east of the Musi estuary. The data showed that the populations of both Sciaenids were higher in the east river mouth rather than in the west. Sciaenid populations were positively correlated with high salinity, DO, chlorophyll a, moderate transparency, and low temperature. A high load of AML’s frequency (7.54 items/m2) and weights (36.8 gram/m2) has reduced both Sciaenid populations in the central river mouth of the estuary. In contrast, low AML loads in the east have correlated with high Sciaenid populations. Model selection based on AIC values shows the best model for P.microdon retained an effect of AML weight with AIC values of 22.591 and 28.321 for O. pama. This concludes that the weight of plastic litter in estuary water was the main limiting factor for Sciaenid populations in Musi.