In this paper, diagnosis for hybrid systems using a parity space approach that considers model uncertainty is proposed. The hybrid diagnoser is composed of modules which carry out the mode recognition and diagnosis tasks interacting each other, since the diagnosis module adapts accordingly to the current hybrid system mode. Moreover, the methodology takes into account the unknown but bounded uncertainty in parameters and additive errors using a passive robust strategy based on the set-membership approach. An adaptive threshold that bounds the effect of model uncertainty in residuals is generated for residual evaluation using zonotopes, and the parity space approach is used to design a set of residuals for each mode. The proposed fault diagnosis approach for hybrid systems is illustrated on a piece of the Barcelona sewer network.