Estimation of a species sensitivity distribution (SSD) by fitting a statistical distribution to ecotoxicity data is a promising approach to deriving “safe” concentrations for microplastics. However, most existing SSDs do not quantitatively consider the diverse characteristics of microplastics, such as particle size and shape. To address this issue, based on 38 mass-based chronic no observed effect concentrations (NOECs) obtained from a recently created database, we estimated SSDs that quantitatively consider the influences of three types of microplastic characteristics (particle length, shape, and polymer type) and habitat of the test species (freshwater vs. marine) by using Bayesian modeling. We selected the best SSD model among all possible models using the widely applicable information criterion. The best SSD model included particle length (range: 0.05–280 μm) and a binary dummy variable corresponding to the fiber shape. Lower chronic NOECs were associated with decreasing particle size and with toxicity tests that included fibers in this model. Combined with the fact that the null model (i.e., an SSD model with no predictor variable) was ranked 27th among the 64 candidate SSD models, our results support the need to incorporate particle characteristics such as length and shape (e.g., fiber) into estimations of SSDs for microplastics. The medians of the hazardous concentration of 5% of species (HC5) for microplastic spheres and fragments, estimated by the posterior distributions of individual parameters in the best SSD model, ranged from 0.02 to 2 µg/L, depending on the particle length (0.1–100 μm). For microplastic fibers, the HC5 values were estimated to be approximately 100 times lower than those for microplastic spheres and fragments with the same particle length. However, the 95% Bayesian credible intervals for HC5 estimates for fibers were considerable, expanded by up to five orders of magnitude. Despite many remaining challenges, the Bayesian SSD modeling utilized in this study provides unique opportunities to simultaneously investigate the influences of multiple microplastic characteristics on the NOECs of multiple species, which would otherwise be difficult to discern.