Diarrhoea is one of the major waterborne diseases spread through the faecal–oral route causing over 10 million cases and over 1,000 deaths in India. This study critically evaluates the interlinkage between bacteriological water quality, i.e. faecal coliforms and diarrhoea cases for the three pre-pandemic years 2017, 2018 and 2019 based on multiple sources. With around 17% of households tap water connectivity as of August 2019, the majority of the Indian population depends on raw groundwater (GW) and surface water sources. For this, faecal coliform (FC) levels in surface and GW have been mapped at district levels using data from India's National Water Quality Monitoring Programme. Health Management Information System's data on diarrhoea have been used to understand the monthly and district-wise variation of diarrhoea. The trends of FC, diarrhoea inpatient cases, and diarrhoea inpatient rates have been discussed. The analysis showed issues associated with the reliability and usefulness of these datasets with 43% of total India districts with no reported FC values for the study period. This study reveals a clear gap in the interlinkage between diarrhoea and bacteriological water quality with the unavailability of granular water quality data as a major challenge.