Artificial neural networks (ANNs) have been applied successfully in various fields. However, ANN models depend on large sets of historical data, and are of limited use when only vague and uncertain information is available, which leads to difficulties in defining the model architecture and a low reliability of results. A conceptual fuzzy neural network (CFNN) is proposed and applied in a water quality model to simulate the Barra Bonita reservoir system, located in the southeast region of Brazil. The CFNN model consists of a rationally-defined architecture based on accumulated expert knowledge about variables and processes included in the model. A genetic algorithm is used as the training method for finding the parameters of fuzzy inference and the connection weights. The proposed model may handle the uncertainties related to the system itself, model parameterization, complexity of concepts involved and scarcity and inaccuracy of data. The CFNN showed greater robustness and reliability when dealing with systems for which data are considered to be vague, uncertain or incomplete. The CFNN model structure is easier to understand and to define than other ANN-based models. Moreover, it can help to understand the basic behaviour of the system as a whole, being a successful example of cooperation between human and machine.