In this study frequency and composition of plankton in Shadegan wetland was carried out in 5 stations during 2007-2008. Genus qualitative identification and their composition and quantitative frequency aspect were studied (for phytoplankton chlorophyll a). Frequency of total 42 genus phytoplankton in 4 classes Bacilariophyceae (Diatom), Cyanophyceae, Chlorophyceae and Dinophyceae are 69.4, 22.22, 10.15 and 5.16 percent respectively and Diatoms are most dominant. In which Cyclotella and Nitzschia genus have the most abundance. In this manner, Frequency of total 24 genus zooplankton 4 groups Rotifera, Copepoda, Protozoa and Cladocera that are 80.47, 17.30, 2 and 0.23 percent respectively and Rotifers are most dominant. Phytoplankton has two frequency peak: first in the summer and the second with less in the early fall. Rogbh and Etysh have the most diversity in all of the stations. Mean annual primary production are 1.67 gC/m²/d and maximum and minimum are 4.67 and 0.50 respectively. Absence of indicator species that eutrohic lakes such as Peridinium and Ceratium and none blooms of Cyanophyceae, are rejected the existence of conditions eutrophic. Other evidence, including presence macrophyta, the low water turbidity and high plankton diversity is an indicator of the quality of all of which are relatively natural wetlands. New input waste water agricultural to wetlands can first increase primary production by high nutrients and according occurrence of chaos theory and environmental stress, stress factors, first increase species diversity and in continuation status diversity decreases .