Human activities along the Amu Darya River have damaged aquatic ecosystems of the Aral Sea Basin. The Khorezm province in northwest Uzbekistan is a productive agricultural area within the basin. The landscape is dotted with small lakes that have formed in natural depressions that receive irrigation runoff water. This study assesses the water quality and ecology of some of these lakes to determine their suitability as sources of irrigation water and income generation from fish production. Since May 2006, water quality and aquatic food web data have been collected and analyzed from 13 of these lakes. Lake salinity ranged from 1 to more than 10 g/L. Few hydrophobic organic contaminants were found in samples collected during the peak of the 2006 growing season, and aquatic species diversity and relative density were low in most lakes. Ongoing research includes estimation of aquatic food web structure and anthropogenic impacts on the ecosystem.