The study measures the relationship between physicochemical variables with the cell density of phytoplankton in different stages of pond – nursery ponds, grow out ponds and brood stock ponds. The study was conducted on nine fish ponds as three from each category of pond at Natore Government Fish Farm in Bangladesh, during the months of January to June in 2012. The observed physicochemical variables– water temperature, transparency, dissolved oxygen, pH, ammonia-nitrogen, total alkalinity and total hardness – were found within the standard ranges. Four groups of phytoplankton– Bacillariophyceae, Chlorophyceae, Cyanophyceae and Euglenophyceae– werefound among the ponds where Euglenophyceae was recorded highest number almost in all ponds over the study period. Total abundance of different groups of phytoplankton was recorded as mean (±SD) cell density (cell/l) 62.77±2.16×104, 47.22±0.69×104, and 77.12±3.42×104 in nursery pond, grow out pond and brood stock pond, respectively. Overall phytoplankton was found better in brood stock pond than others. Total phytoplankton density has been exhibited significantly positive correlation with DO and inverse relation with water temperature, pH, ammonia-nitrogen and total alkalinity in case of nursery pond. In case of grow out pond, total phytoplankton density has been exhibited significantly positive correlation with temperature and transparency, and significantly negative correlation with others physicochemical characteristics. In case of brood stock pond, total phytoplankton density has no significant relationship with any physicochemical variables of water.