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In this study, trophic state indicators, total phosphate, algal chlorophyll and Secchi disk transparency and zooplankton community of Lake Choghakhor was studied monthly between May 2003 and April 2004. This lake is a shallow ecologically and economically important water body in eastern part of Iran. Crop farming and recreational activities are examples of the human impact around and within the lake, leading to a loading of DIN (Dissolved Inorganic Nitrogen) and TP (Total Phosphate) into the lake. Now submerged plants especially Myriophyllum spicatum has covered almost the entire lake and dense macrophyte beds (Polygonom amphibium), located on the East Southern end of the lake appear to act as a sink for these nutrients. Lake Choghakhor appeared to be in a macrophyte dominated clear water state with low TP (annual mean: 24 +/- 15 microg L(-1)) and chlorophyll a (annual mean: 3 +/- 1.28 microg L(-1)) concentrations and very high Secchi depth. The grazing pressure of dominant pelagic filtering zooplankton Daphnia longespina did not seem to be significant in determining the low phytoplankton crop expressed as chlorophyll a. We expect that sequestering of nutrients by submerged plants and associated epiphytes are the dominant stabilizing mechanisms suppressing the phytoplankton crop of Lake Choghakhor.