Pollution of inland waters by agricultural land use is a concern in many areas of the world, and especially in arid regions, where water resources are inherently scarce. This study used physical and chemical water quality and stable nitrogen isotope (δ15N) measurements from zooplankton to examine nitrogen (N) sources and concentrations in four small lakes of Khorezm, Uzbekistan, an arid, highly agricultural region, which is part of the environmentally-impacted Aral Sea Basin. During the 2-year study period, ammonium concentrations were the highest dissolved inorganic N species in all lakes, with a maximum of 3.00 mg N l−1 and an average concentration of 0.62 mg N l−1. Nitrate levels were low, with a maximum concentration of 0.46 mg N l−1 and an average of 0.05 mg N l−1 for all four lakes. The limited zooplankton δ15N values did not correlate with the high loads of synthetic fertilizer applied to local croplands during summer months. These results suggest that the N cycles in these lakes may be more influenced by regional dynamics than agricultural activity in the immediate surroundings. The Amu-Darya River, which provides the main source of irrigation water to the region, was identified as a possible source of the primary N input to the lakes.