This study examines an improved and simplified method for solid-phase extraction (SPE), which offers rapid and accurate determination and identification of 44 pharmaceutically active compounds using ultra-performance liquid chromatography (UPLC) and tandem mass spectrometry (MS/MS). The common active compounds include four macrolides, seventeen sulfonamides, four quinolones, chloramphenicol, eight β-lactams, four tetracyclines, lincomycin, amantadine, 4-acetamidophenol, phenylbutazone, trimethoprim, clenbuterol, and hydrocortisone in water samples. We optimized crucial parameters of MS/MS, UPLC, and SPE and studied the matrix effect related to the modified analytical process from water samples. The matrix-matched calibration curves were accomplished at seven concentration levels and a satisfactory linear relationship ( r 2 > 0.994) was observed within the range of 0.1–500 ng/mL. Results show varying limits of detection (0.0111–0.966 ng/L for different analytes based on signal-to-noise (S/N) = 3) and limits of quantitation (0.0382–3.26 ng/L). Recoveries of the spiked samples ranged from 75.7 to 108% with relative standard deviation lower than 9.6%. The proposed method was successfully applied to the analysis of real samples.