Contamination with Cryptosporidium and Giardia from drinking water sources in a city in Northern India was assessed. A protocol modified from a standard ISO protocol, which includes filtration, concentration, separation and detection steps, was tested and showed comparable recovery efficiencies (Giardia mean = 77.4%, Cryptosporidium mean = 61.8% from the modified protocol, compared with Giardia mean = 61.6%, Cryptosporidium mean = 69% from the ISO protocol) at a substantial cost reduction. This protocol was used for analysing 71 samples of potable water from different areas of Chandigarh, where sampling locations were divided into groups according to the population density, which also partially equates with the level of infrastructure. Samples were collected during (n = 29) and outside the monsoon season (n = 42). Of all samples analysed, 16 (22.5%) were Cryptosporidium- and/or Giardia-positive. Parasites per sample were low (1–10 (oo)cysts per 10 L), although one sample contained large numbers of Giardia cysts (>1,000). Polymerase chain reaction analyses on the small subunit ribosomal ribonucleic acid (SSU rRNA), triose-phosphate isomerase (tpi), glutamate dehydrogenase (gdh) and beta-giardin (bg) gene sequences on Giardia-positive samples and SSU rRNA on Cryptosporidium-positive samples tended to be unsuccessful, although Giardia cysts of Assemblages B and C were identified. No association with the season was detected, but an association with the location of water supply was identified. Samples from areas with the lowest infrastructure were not associated with higher levels of contamination, but samples from the middle level were significantly more likely to be contaminated than those from the highest level of infrastructure. Results indicate that even in a city with a well-developed infrastructure, the contamination of potable water with protozoan parasites remains a public health risk.