The increase in synthesis and application of silver nanoparticles (AgNPs) in the last decade has resulted in contamination of AgNPs in the aquatic environment. The presence of AgNPs in aquatic environments has posed toxic effects to aquatic organisms and ecological damage. In this study, two tropical microalgae species including the freshwater Scenedesmus sp. and the marine diatom Thalassiosira sp. were employed to examine the toxic effects of AgNPs. The toxic effects were determined by analyzing different end points, such as half maximal effective concentration (EC50), algae growth inhibition, algae cell size, chlorophyll-a content, and total lipid accumulation. The results suggested that AgNPs presented different toxicity mechanisms for microalgae and showed to be more toxic in freshwater than in marine environment. The EC50 values of AgNPs after 72 h for the growth inhibition of Scenedesmus sp. and Thalassiosira sp. were 89.92 ± 9.68 and 107.21 ± 7.43 μg/L, respectively. AgNPs at a certain concentration have resulted in change in cell diameter, reduction in chlorophyll-a content, and enhancement of the total lipid production in the tested microalgae. Thus, local species should be involved in the toxic assessment. This research contributes on understanding the toxicity of AgNPs on freshwater and marine environments.