This chapter is devoted to the discussion of multiscale modeling ofprocesses occurring during the deposition of nanoparticles on surfaces. The modeling relies on the method of stochastic dynamics. Stochastic dynamics describes processes in complex systems where the dynamics is represented through a number of kinetic processes occurring with certain probabilities. The chapter discusses the concept of stochastic dynamics and illustrates its implementation in a popular program MBN Explorer. In MBN Explorer, stochastic dynamics relies on the Monte Carlo approach and describes physical, chemical, and biological processes on multiple temporal and spatial scales. The chapter presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several computational case studies accompanied with characteristic experimental results to validate the computational approaches.