The legacy of Soviet-era agricultural practices in Central Asia has contributed to severe environmental degradation through residual organochlorine pesticide contamination, dramatic reduction in surface water, and the near-total desiccation of the Aral Sea. Few studies have investigated hazards to human health, despite the region’s elevated burden of disease. This study aimed to characterize environmental hazards in the Republic of Karakalpakstan, one of the most environmentally and economically impacted regions. Environmental assessment included the collection of 140 soil, water, and sediment samples across 79 unique locations. Pesticide results showed organochlorine pesticides over US reference levels in 100% of water samples, with 30% also exceeding in hexavalent chromium. Water salinity is a primary concern: expressed as total dissolved solids, values ranged from 563 to 3852 mg/L. Over half of the 46 soil and sediment samples tested above reference levels for aldrin. Soil and sediment sample salt content reached up to 8.7%. Residual persistent organochlorine pesticides remain a significant health risk in Karakalpakstan, while water availability is decreasing, and water quality parameters, including salinity, dissolved oxygen, pH, dissolved metals, and nitrate levels, are degrading. Such challenges extend beyond the Aral Sea Basin: as salinization and desiccation of endorheic lakes continue on a global scale, similar situations may become commonplace. Research and interventions from this region can serve to support other similarly impacted areas.