More than quarter of underprivileged global population, who lack access to basic sanitation and clean drinking water, live in India. Consequently, every year, millions suffer with enteric diseases from drinking faecal-contaminated groundwater. The UN Sustainable Development Goal lists access to safe water and basic sanitation for all by 2030, as their sixth goal. For the first time, the role of economic improvement on decrease in water-borne faecal pathogens was studied across Indo-Ganges–Brahmaputra river basin (IGB) for almost last three decades, to delineate the long-term improvement trends of groundwater quality across India, as a consequence of development. Long-term temporal (1990–2017) and high-resolution spatial (administrative block scale, n$=$2217) datasets of water-borne faecal pathogen concentration in groundwater and satellite-based nightlight (NL) were used to investigate the statistical trends and causal relationships. Linear and nonlinear (Hodrick–Prescott) trend analyses, panel data analyses, Bayesian vector autoregression (VAR) and lead–lag causality (LLC) analyses were performed on aforesaid culled datasets. However, the efficiency of development in alleviating the water quality and public health, and relationship with economic development, has not been well understood. Here, for the first time, using long-term, high-spatial resolution (n$=$2217), annual in-situ measurements and multivariate statistical models, we show that the spatially variable groundwater faecal pathogen concentration (FC, 2002–2017, $-$1.39 $\pm$ 0.01%/yr) has been significantly decreased across the basin. In most areas, increasing satellite-based NL plays a significant role (NL, 1992–2013, 3.05 $\pm$ 0.01%/yr) in reduction of FC. However, in areas with low literacy rate surpass development. Enhanced decrease of faecal coliform concentration in groundwater possibly signifies the implementation of Clean India Mission since 2014.