Cryptosporidium is a protozoan parasite that can cause diarrhoea. Human faeces are an important source of Cryptosporidium in surface waters. We present a model to study the impact of sanitation, urbanization and population growth on human emissions of Cryptosporidium to surface waters. We build on a global model by Hofstra et al (2013 Sci. Total Environ. 442 10–9) and zoom into Bangladesh and India as illustrative case studies. The model is most sensitive to changes in oocyst excretion and infection rate, and to assumptions on the share of faeces reaching the surface water for different sanitation types. We find urban centres to be hotspots of human Cryptosporidium emissions. We estimate that 53% (Bangladesh) and 91% (India) of total emissions come from urban areas. 50% of oocysts come from only 8% (Bangladesh) and 3% (India) of the country area. In the future, population growth and urbanization may further deteriorate water quality in Bangladesh and India, despite improved sanitation. Under our 'business as usual' ('sanitation improvements') scenario, oocyst emissions will increase by a factor 2.0 (1.2) for India and 2.9 (1.1) for Bangladesh between 2010 and 2050. Population growth, urbanization and sanitation development are important processes to consider for large scale water quality modelling.