The present paper deals with an estimation of the water quality of the Struma river. Long-term trends, seasonal patterns and data set structures are studied by the use of statistical analysis. Nineteen sampling sites along the main river stream and different tributaries were included in the study. The sites are part of the monitoring net of the region of interest. Seventeen chemical indicators of the surface water have been measured in the period 1989–1998 in monthly intervals. It is shown that the water quality is relatively stable throughout the monitoring period, which is indicated by a lack of statistically significant trends for many of the sites and by chemical variables. Several seasonal patterns are observed at the sampling sites and four latent factors are identified as responsible for the data set structure.