The upstream area of the watershed has high rainfall, resulting in large volumes of runoff and peak discharge. The runoff discharge causes soil erosion, transporting soil particles by the flow and eventually settling as sedimentation. This sedimentation leads to river siltation and narrowing. Additionally, high-flow discharge causes turbulence and flooding. This research aimed to predict sedimentation rates due to land erosion in the watershed using the GIS-based Modified Universal Soil Loss Equation (MUSLE). The study was conducted in the Krueng Peuto sub-watershed in Indonesia. The interphase modeling revealed that the highest land sedimentation rate in the Krueng Peuto watershed occurred in 2015, with the sediment of 40,503.10 Mg.y−1, while the least was in 2013, with 2,006.52 Mg.y−1 of sediment. The results indicate that surface runoff has the most significant influence on land sedimentation. The rate of soil loss is closely related to land conservation practices, with poorly vegetated land contributing the most to surface runoff. Water flow velocity and its destructive power erode the soil into tiny grains, transported and deposited as sedimentation in the river. The MUSLE’s capability in identifying erosion-prone areas and predicting sediment yield based on rainfall events is crucial for effective sediment management planning. Implementing long-term land conservation measures is essential to preserve land capacity effectively.