Membrane transporters play a crucial role in determining fate of administered drugs in a biological system. Early identification of plausible transporters for a drug molecule can provide insights into its therapeutic, pharmacokinetic, and toxicological profiles. In the present study, predictive models for classifying small molecules into substrates and nonsubstrates of various pharmaceutically important membrane transporters were developed using quantitative structure-activity relationship (QSAR) and proteochemometric (PCM) approaches. For this purpose, 4575 substrate interactions for these transporters were collected from the Metabolism and Transport Database (Metrabase) and the literature. The transporters selected for this study include (i) six efflux transporters, viz., breast cancer resistance protein (BCRP/ABCG2), P-glycoprotein (P-gp/MDR1), and multidrug resistance proteins (MRP1, MRP2, MRP3, and MRP4), and (ii) seven influx transporters, viz., organic cation transporter (OCT1/SO22A1), peptide transporter (PEPT1/SO15A1), apical sodium-bile acid transporter (ASBT/NTCP2), and organic anion transporting peptides (OATP1A2/SO1A2, OATP1B/SO1B1, OATP1B3/SO1B3, and OATP2B1/SO2B1). Various types of descriptors and machine learning methods (classifiers) were evaluated for the development of robust predictive models. Additionally, ensemble models were developed by bagging of homogeneous classifiers and selective fusion of heterogeneous classifiers. It was observed that the latter approach improves the accuracy of substrate/nonsubstrate prediction for transporters (average correct classification rate of more than 0.80 for external validation). Moreover, structural fragments important in determining the substrate specificity across the various transporters were identified. To demonstrate these fragments on the query molecule, contour maps were generated. The prediction efficacy of the developed models was illustrated by a good correlation between the reported logBB value of a molecule and its predicted substrate propensity for blood-brain barrier transporters. Conclusively, this comprehensive modeling analysis can be efficiently employed for the prediction of membrane transporters of a drug, thereby providing insights into its pharmacological profile.