Researchers recognize that ionization state may influence the biological activity of weak acids and bases. Dissociation in aqueous solutions is controlled by the pKa of a compound and the pH of the matrix. Because many pharmaceuticals are implicitly designed as ionizable compounds, site-specific variability in pH of receiving waters may introduce uncertainty to ecological risk assessments. The present study employed 48-h and 7-d toxicity tests with Pimephales promelas exposed to the model weak base pharmaceutical sertraline over a gradient of environmentally relevant surface water pHs. The 48-h experiments were completed in triplicate, and the average lethal concentration values were 647, 205, and 72 μL sertraline at pH 6.5, 7.5, and 8.5, respectively. Survivorship, growth, and feeding rate (a nontraditional endpoint linked by other researchers to sertraline's specific mode of action) were monitored during the 7-d experiment. Adverse effects were more pronounced when individuals were exposed to sertraline at pH 8.5 compared to pH 7.5 and 6.5. The pH-dependent toxicological relationships from these studies were related to in-stream pH data for two streams in the Brazos River basin of central Texas, USA. This predictive approach was taken because of the scarcity of environmental analytical data for sertraline. The results of this study emphasized temporal variability associated with in-stream pH linked to seasonal differences within and between these spatially related systems. Relating site-specific pH variability of surface waters to ionization state may allow researchers to reduce uncertainty during ecological risk assessment of pharmaceuticals by improving estimates of biological effects associated with exposure.