The application of herbicides in rice fields necessitates an understanding of their effects on non-target organisms, particularly cyanobacteria, which serve as primary producers in the ecosystem. This study examined the impact of commercial paraquat and butachlor formulations on the paraquat-tolerant cyanobacterium, Nostoc sp. N1 and its intricate interactions during the growth of rice seedlings. The research evaluated the acute toxic response of Nostoc sp. N1 to herbicides, subsequently conducting 7 day germination and 21 day pot experiments to determine the mitigating or synergistic effects of Nostoc sp. N1 in simultaneously exposed rice seedlings. Initially, the study evaluated baseline toxicity, demonstrating that paraquat (median inhibitory concentrations EC50=0.241 mg L-1) exhibited significantly higher toxicity to Nostoc sp. N1 than butachlor (EC50=2.074 mg L-1). Subsequent physiological assays revealed two significant and opposing results. First, Nostoc sp. N1 responded differently to the herbicides; paraquat caused dose-dependent inhibition of growth, chlorophyll-a, and phycocyanin, while butachlor improved biomass accumulation and chlorophyll-a production, while only concurrently reducing the phycocyanin content at high doses. Second, differential responses resulted in contrasting findings in rice seedlings. Specifically, Nostoc sp. N1 demonstrated efficacy as a mitigating agent against paraquat, showing dose-dependent protection in the 7 day germination assay and providing complete defense in the 21 day experiment by restoring various physical and biochemical parameters. In contrast, Nostoc sp. N1 demonstrated a significant synergistic negative effect with butachlor in the 7 day assay, significantly enhancing its toxicity at all concentrations. This developed in the 21 day experiment into only partial mitigation, in which Nostoc sp. N1 restored biochemical stress indicators (such as amino acids) but did not recover physical growth. Based on these results, cyanobacterial bio-inoculants might not be uniformly advantageous and their use should be herbicide-specific. Although Nostoc sp. N1 is a potential agent for paraquat bioremediation, its incompatible interaction with butachlor could inadvertently accelerate crop damage.