The purpose of this work is to extend the analysis of the Smith predictor structure to multiple input multiple output (MIMO) systems with uncertain multiple delays. This is applied to the set of models that can be factorized into a rational MIMO model in series with left/right diagonal (multiple) delay matrices. Necessary and sufficient conditions on the plant's model to achieve this factorization are proved. This factorized structure is instrumental for the structured robustness analysis and applies to multiple pool open flow canals. Nominal and robust performance and stability are analyzed for the case of plants with multiple uncertain delays for two different uncertainty structures: global dynamic and structured parametric. The first uncertainty structure could also accommodate the dynamic uncertainty of the plant's rational part as well. This analysis is applied to a controller designed for a two-pool canal system. (C) 2008 Elsevier Ltd. All rights reserved.