Controlled Environment Agriculture (CEA), including hydroponics, aquaponics, aeroponics, and greenhouse cultivation, is rapidly expanding as a strategy to enhance food security under increasing pressures from climate change, urbanization, and growing global food demand. Water is fundamental to ecosystem services, agricultural productivity, economic resilience and human health, yet it is a finite resource that is becoming increasingly scarce and vulnerable to degradation from anthropogenic pollution. Although CEA substantially reduces freshwater consumption and enables year-round crop production, its dependence on recirculating water systems creates distinct food safety challenges that are not adequately addressed within existing public health and regulatory frameworks. Unlike conventional soil-based agriculture, water in CEA serves simultaneously as the medium for nutrient delivery, microbial transport, and pathogen dissemination, allowing contaminants introduced at a single point to spread rapidly throughout an entire production system. Despite epidemiological evidence identifying leafy greens as major vehicles of foodborne illness, outbreak surveillance rarely distinguishes between conventionally and CEA-produced crops, limiting attribution of waterborne risks. Here, we synthesize evidence from environmental microbiology, food safety, epidemiology, and agricultural sciences to evaluate water quality as a central determinant of food safety in CEA. We identify critical gaps in surveillance, microbial risk assessment, monitoring technologies, and regulatory oversight, and propose an integrated framework for water quality management that aligns food safety with sustainable water stewardship. As CEA becomes an increasingly important component of global food production, strengthening water governance and surveillance will be essential to safeguarding public health while realizing the sustainability benefits of water-efficient agriculture.