This paper presents a set of tools developed to support an innovative methodology to design and upgrade wastewater treatment systems in a probabilistic way. For the first step, data reconstruction, two different tools were developed, one for situations where data are available and another one where no data are available. The second step, modelling and simulation, implied the development of a new simulation platform and of distributed computation software to deal with the simulation load generated by the third step, uncertainty analysis, with Monte Carlo simulations of the system over one year, important dynamics and stiff behaviour. For the fourth step, evaluation of alternatives, the evaluator tool processes the results of the simulations and plots the relevant information regarding the robustness of the process against input and parameters uncertainties, as well as concentration-duration curves for the risk of non-compliance with effluent and receiving water quality limits. This paper illustrates the merits of these tools to make the innovative methodology of practical interest. The design practice should move from conventional procedures suited for the relatively fixed context of emission limits, to more advanced, transparent and cost-effective procedures appropriate to cope with the flexibility and complexity introduced by integrated water management approaches. (c) 2008 Elsevier Ltd. All rights reserved.