The species sensitivity distribution (SSD) calculates the hazardous concentration at which 5% of species (HC5) will be potentially affected. For many compounds, HC5 values are unavailable impeding the derivation of SSD curves. Through a detailed bibliographic survey, we selected HC5 values (from acute toxicity tests) for freshwater aquatic species and 129 pesticides. The statistical distribution and variability of the HC5 values within the chemical classes were evaluated. Insecticides are the most toxic compounds in the aquatic communities (HC5 = 1.4 × 10−3 µmol L−1), followed by herbicides (HC5 = 3.3 × 10−2 µmol L−1) and fungicides (HC5 = 7.8 µmol L−1). Subsequently, the specificity of the mode of action (MoA) of pesticides on freshwater aquatic communities was investigated by calculating the ratio between the estimated baseline toxicity for aquatic communities and the HC5 experimental values gathered from the literature. Moreover, we proposed and validated a scheme to derive the ecological thresholds of toxicological concern (eco-TTC) of pesticides for which data on their effects on aquatic communities are not available. We proposed eco-TTCs for different classes of insecticides, herbicides, and fungicides with a specific MoA, and three eco-TTCs for those chemicals with unavailable MoA. We consider the proposed approach and eco-TTC values useful for risk management purposes.