This study discusses research that develops a general framework and presents a specific implementation of a stochastic modelling system, using linked overland flow and routing simulation models. The specific implementation uses the Gridded Surface Sub-surface Hydrological Analysis (GSSHA) overland flow model, and the reservoir routing and quality model CE-QUAL-W2, to develop the stochastic modelling system. For stochastic simulations, modellers can define up to six GSSHA parameters for stochastic treatment, select the appropriate probability density functions and range, and determine the number of runs in the simulation. The tools described herein then create the correct input and output files, run the linked simulation models using the defined stochastic parameters, and aggregate the voluminous results. Interactive tools were developed to compute credible intervals from the results, and create reports that present the variability in a manner that is easily understood and communicated. Model set-up and development, stochastic and statistical parameter input, stochastic simulation execution and results analysis were implemented using the Watershed Modeling System, model pre-and postprocessing system. This study presents the tools, algorithms and user interfaces developed to implement the linked stochastic modelling system, as well as a simple example demonstrating the tools and the type of analysis supported by this system.