This paper examines the relationships between watercourse typology and selected indicators of long-term surface water quality for rivers in the Czech Republic. The parameters used to define watercourse typology are in accord with the Water Framework Directive 2000/60/EC outlined by the European Commission. The relationships were tested using descriptive and multivariate statistical analysis, namely cluster analysis and canonical correspondence analysis. It was found that only some of the typological parameters have a close association with indicators of surface water quality. Specifically, the parameters of altitude and geology show clear relationships with pH, calcium content, and the saprobity index of macroinvertebrates. Conversely, parameters that are strongly influenced by anthropogenic pollution show weak relationships with indicators of surface water quality. These depend instead on the presence of pollution sources rather than on natural environmental conditions.