Spilled oil in inland waterways can aggregate with mineral and organic particles to form oil-particle aggregates (OPAs). OPAs can be transported in suspension or deposited to the bed. Modeling the fate and transport of OPAs can provide useful information for making mitigation decisions. A novel open-source tool, FluOil, is developed to predict where OPAs may deposit and when they arrive in affected river/lake reaches by implementing the random walk particle tracking algorithm to represent the advection, diffusion, deposition, and resuspension of OPAs. The usability of FluOil is demonstrated with the 2010 Kalamazoo River oil spill case study. An unsteady hydrodynamic model simulates the river hydraulics and provides hydraulic data for use in FluOil. Settling velocity and critical shear stress for resuspension are the most important OPA properties concerning the transport and deposition of OPAs. Settling velocity determines the vertical distribution of OPAs and, thus, the travel speed, whereas critical shear stress determines where and when OPAs are deposited and resuspended.