Particle tracking models (PTMs) can simulate the dispersal of particulate and dissolved material in the marine environment that are difficult to observe directly – including organic matter and pollutants that may change in composition, biological organisms that can grow and swim, and pathogens that decay and attach to other material. However, the predicted dispersal patterns can carry significant uncertainties, arising from factors such as the accuracy of the driving hydrodynamics, PTM resolution, stochasticity of dispersal simulations, and parameterisation of the behavioural characteristics of the particles (e.g., microplastic settling speeds, eDNA decay, larval swimming behaviour). Numerous PTM software packages are available, offering different parameterisations, meaning that selecting an appropriate PTM to minimise model uncertainties and optimise computational efficiency is important. This review provides a foundational resource and best practices for PTM users, particularly for marine applications. It outlines essential questions that users should ask to help choose the appropriate PTM, and its parameterisation for the intended application. A case study is presented to illustrate potential uncertainties in particle dispersal using three different PTMs. The case study highlights that, in regions with complex coastlines, the land boundary condition can significantly impact particle trajectories and requires careful consideration. This resource will help standardise good practices for configuring PTMs to accurately represent (or account for uncertainty in) dispersal in the marine environment.