The objective of the research presented in this paper is to develop an algorithm for predicting behaviour of complex technical systems in an uncertain working environment. System's dynamic behaviour modelling and simulation should help to develop new and improve existing architectures of complex technical systems by mapping in both directions, from the structural to the behavioural domain and vice versa. The algorithm for predicting behaviour during system's architecture development consists of several operations shortly described in this paper. The proposed algorithm was verified on an example of a complex technical system - an air-handling unit.