The aim of this work is to introduce a Tailor-Made-Protocol (TMP) to assess water quality for irrigation canals in accordance to monitoring objectives that deal with pollutant concentrations and loads. The water quality/quantity data collected monthly from 2008 to 2016 for the El-Nubaria canal catchment in Egypt was used as a case study. The developed protocol includes a series of statistical tools employed to facilitate better handling of the collected data and then transform it into useful information. These tools included descriptive statistics and checking compliance with standards, percentage analysis and showing the pollutant loads using box and whisker plots. Finally, cluster analysis was employed to classify the monitoring locations into a number of groups that have similar water quality conditions. The derived clusters were then visualized by using the Geographical Information System (GIS) to draw thematic maps. The success in applying the proposed TMP showed its effectiveness and applicability to check compliance with water quality standards and allocate waste loads from different sources as well as classifying water quality status.