Background: An epidemic of chronic kidney disease is occurring in rural communities in low-income and middle-income countries that do not share common kidney disease risk factors such as diabetes and hypertension. This chronic kidney disease of unknown etiology occurs primarily in agricultural communities in Central America and South Asia. Consequently, environmental risk factors including heat stress, heavy metals exposure, and low altitude have been hypothesized as risk factors. We conducted an environmental epidemiological analysis investigating these exposures in India which reports the disease. Methods: We used a random sample population in rural and urban sites in Northern and Southern India in 2010, 2011, and 2014 (n = 11,119). We investigated associations of the heat index, altitude, and vicinity to cropland with estimated glomerular filtration rate (eGFR) using satellite-derived data assigned to residential coordinates. We modeled these exposures with eGFR using logistic regression to estimate the risk of low eGFR, and linear mixed models (LMMs) to analyze site-specific eGFR-environment associations. Results: Being over 55 years of age, male, and living in proximity to cropland was associated with increased risk of low eGFR [odds ratio (OR) (95% confidence interval (CI) = 2.24 (1.43, 3.56), 2.32 (1.39, 3.88), and 1.47 (1.16, 2.36)], respectively. In LMMs, vicinity to cropland was associated with low eGFR [-0.80 (-0.44, -0.14)]. No associations were observed with temperature or altitude. Conclusions: Older age, being male, and living in proximity to cropland were negatively associated with eGFR. These analyses are important in identifying subcommunities at higher risk and can help direct future environmental investigations.