The increasing presence of active pharmaceutical ingredients (APIs) in aquatic ecosystems, driven by widespread human use, poses significant risks, including acute and chronic toxicity to aquatic species. However, the scarcity of experimental toxicity data on APIs and related compounds due to the high costs, time requirements, and ethical concerns associated with animal testing hinders comprehensive risk assessment. In response, we developed quantitative structure-toxicity relationship (QSTR) and interspecies quantitative structure toxicity-toxicity relationship (i-QSTTR) models for three key aquatic species: zebrafish, water fleas, and green algae, using NOEC as an endpoint, following OECD guidelines. Algae, daphnia, and fish, recognized as standard organisms in toxicity testing, are crucial bio-indicators due to their size, transparency, adaptability, and regulatory acceptance. We used partial least squares (PLS) and multiple linear regression (MLR) methods for model development alongside machine learning techniques such as Random Forest (RF), Support Vector Machines (SVM), K-nearest Neighbor (kNN), and Neural Networks (NN) to enhance the predictivity. Lipophilicity, electronegativity, unsaturation, a molecular cyclized degree in molecular structure, large fragments, aliphatic secondary C(sp2), and R–CR–R groups were identified as critical biomarkers for API toxicity. Screening of the PPDB (pesticide properties databases) and DrugBank validated the practical application of these models, offering valuable tools for regulatory decisions, safer API design, and the preservation of aquatic biodiversity.