Food cooking practices and water sources have been associated with increased risk of cancer, mainly through exposure to carcinogens such as heterocyclic amines (HCAs), polycyclic aromatic hydrocarbons (PAHs) and nitrates. Using data from the Golestan case-control study, conducted between 2003 and 2007 in a high-risk region for esophageal squamous cell carcinoma (ESCC), we sought to investigate the association between food preparation and drinking water sources and ESCC. Information on food preparation methods, sources of drinking water and dietary habits were gathered from 300 cases and 571 controls individually matched for age, sex and neighborhood using a structured questionnaire and a semi-quantitative food frequency questionnaire, respectively. Multivariate conditional logistic regression was used to estimate odds ratios (OR) adjusted for potential confounders and other known risk factors including socioeconomic status and smoking. More than 95% of the participants reported using meat, mostly red meat. Red meat consumption above 75th percentile increased the odds of ESCC by 2.1 fold (95% confidence interval (CI): 1.2, 3.6). On the other hand, fish intake was associated with a significant 70% decrease in ESCC odds (0.4, 0.8). Among meat users, ORs (95% CI) for frying meat (red or white) and fish were 2.9 (1.6, 5.7) and 2.3 (1.3, 4.1), respectively. Drinking unpiped water increased the odds of ESCC by 4.3 times (2.2, 8.1). The OR for each 10-year increase in the duration of drinking unpiped water 1.5 (1.2, 1.8). Our results suggest independent roles for red meat intake, drinking water source, and food preparation method in ESCC.