Limited data exist on the interactions between nanoplastics (NPs) and co-contaminants under diverse environmental conditions. Herein, a factorial composite toxicity analysis approach (FCTA) was developed to analyze the time-dependent composite effects of NPs (0 ∼ 60 mg/L), copper (Cu, 0.2 ∼ 6 mg/L) and phenanthrene (PHE, 0.001 ∼ 1 mg/L) on microalgae under diverse pH (6.7 ∼ 9.1), dissolved organic matter (DOM, 1.5 ∼ 25.1 mg/L), salinity (1 ∼ 417 mg/L) and temperature (23 ∼ 33 °C) within the Canadian prairie context. The toxic mechanism was revealed by multiple toxic endpoints. The combined toxicity of NPs, Cu and PHE within prairie aquatic ecosystems was assessed by the developed FCTA-multivariate regression model. Contrary to individual effects, NPs exhibited a promotional effect on microalgae growth under complex environmental conditions. Although Cu and PHE were more hazardous, NPs mitigated their single toxicity. Environmental conditions and exposure times significantly influenced the main effects and interactions of NPs, Cu and PHE. The synergistic effect of NPs*Cu and NPs*PHE on microalgae growth became antagonistic with increased pH or DOM. Microalgae in the Souris River, Saskatchewan, were projected to suffer the most toxic effects. Our findings have significant implications for the risk management of NPs.