Abstract Sturgeons are the most valuable aquatic animals in the Caspian Sea. Sturgeon fries at 100 mg weight easily trapped in heavy dense stands of submerged aquatic vegetation. Due to the often detrimental impacts of submerged weeds on growth and mortality of young fish, removal of nuisance vegetation with minimal harm to sturgeon fries is a desirable goal. Paraquat (1,1´-dimethyl-4, 4´-bipyridinium ion) was evaluated at rates of 0, 0.5, 1, 2, 5, and 10 mg L-1 in the fish ponds for control of Potamogeton crispus, Ceratophyllum demersum, Myriophyllum spicatum and Hydrilla verticillata in the International Institute of Caspian Sea, Shahid Ansari and Shahid Beheshti Fish Research Stations, Rasht, Iran during 2011-2012. Paraquat treatments were conducted on May 25, 2011 and June 10, 2012. The 5 mg L-1 treatments and above reduced biomass of all aquatic weeds by > 75%. Treatment of 10 mg L-1 reduced the biomass of aquatic weeds by > 90%; however this application rate also significantly reduced growth several desirable and non-target species such as Chara by > 90%. Biomass of submerged weeds following the 0.5, 1, 2 mg L-1 application of paraquat were reduced 8, 12 and 26% respectively. Results showed the removal of competitive, canopy forming weeds such as Potamogeton crispus, Ceratophyllum demersum and Myriophyllum spicatum open new areas and increased the survivability rate of sturgeon fries by 45%.