Wastewater irrigation using sewage and water from polluted sources is widespread in Kathmandu Valley, Nepal. Data on the prevalence of pathogens in irrigation sources are important for assessing the health risks for both farmers and consumers. In this study, 13 and 15 water samples were collected during the rainy (September 2014) and dry (April 2015) seasons, respectively, from irrigation sources [river water (n = 17), sewage (n = 5), pond water (n = 3), canal water (n = 1), and effluent of a wastewater treatment plant (WWTP; n = 2)] in Kathmandu Valley. Based on fluorescence microscopy, all the analyzed samples (n = 19) tested positive for Giardia, whereas 68% tested positive for Cryptosporidium. In addition, indicator bacteria (Escherichia coli and total coliforms) were detected in all samples (n = 28), with significantly higher concentrations during the dry season than during the rainy season (t-test, p < 0.05). Indicator bacteria and protozoan concentrations were abundant in sewage and river water samples and comparatively less in the remaining samples. Positive correlations between indicator bacteria and protozoa concentrations suggested that E. coli and total coliforms could be considered as rough indicators of protozoa contamination of wastewater irrigation sources.