Neural networks can provide effective predictive models for complex processes that are poorly described by first principle models, such as wastewater biological treatment systems. In this paper multilayer perceptron (MLP) and functional-link neural networks (FLN) are developed to predict inlet and outlet biochemical oxygen demand (BOD) of an aerated lagoon operated by International Paper of Brazil. In Part 1, predictive models for both inlet and outlet BOD for the aerated lagoon were developed using linear multivariate regression techniques. For the current case study, MLP networks are the best choice for the prediction models. When only a relatively small number of samples is available, substantial improvement in inlet and outlet BOD prediction is shown for both FLN and MLP modeling using a reduced input variable set that was generated using partial least squares (PLS). Thus, this paper provides a novel approach for developing PLS-FLN model structures. (C) 2004 Elsevier B.V. All rights reserved.105416716169