The adverse effects of chemical nitrogen fertilizers affecting soil fertility, water pollution and native microorganisms, particularly cyanobacteria, in wetland rice cultivation have drawn global attention towards the use of alternative sources like N2-fixing cyanobacteria as a biofertilizer for sustainable rice farming. Although chemical nitrogen fertilizers are extensively used for obtaining higher rice yield, they are likely to have a deleterious effect on the growth and N2-fixation of diazotrophs, including cyanobacteria. In addition, biocides (herbicides and insecticides) are widely being used in rice cultivation for optimizing crop yield, but these chemicals also affects non-target organisms adversely. There are several reports indicating impacts of these agrochemicals on cyanobacteria, but most such studies were carried out under laboratory conditions. This article reviews information from different field evaluations on the impact of agrochemicals on cyanobacteria along with rice crop in wetland rice field ecosystem.