We propose a new data mining process to extract original knowledge from hydro-ecological data, in order to help the identification of pollution sources. This approach is based (1) on a domain knowledge discretization (quality classes) of physico-chemical and biological parameters, and (2) on an extraction of temporal patterns used as discriminant features to link physico-chemistry with biology in river sampling sites. For each bio-index quality value, we obtained a set of significant discriminant features. We used them to identify the physico-chemical characteristics that impact on different biological dimensions according to their presence in extracted knowledge. The experiments meet with the domain knowledge and also highlight significant mismatches between physico-chemical and biological quality classes. Then, we discuss about the interest of using discriminant temporal patterns for the exploration and the analysis of temporal environmental data such as hydro-ecological databases.