Solid-phase microextraction (SPME) coupled to liquid chromatography with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) has been widely used to analyze biological fluids, tissues, and environmental matrixes for a variety of organic compounds including pharmaceuticals. However, effects of the sample matrix coextracted by SPME on tandem mass spectrometry analysis have not been systematically investigated. In this study, we characterized the complexity of matrix effects (ME) by analyzing SPME extracts of fish muscle and brain tissue, blood, and bile, as well as tap water, surface water, and the influent and effluent from a wastewater treatment plant. Significant enhancement or suppression of ionization (>15%) was observed with all biological and environmental samples. Intrasample ME variability was assessed through comparison of multiple samples from the same sample matrix, while intersample variability between different experimental subjects or varying sample treatment, storage, and sampling conditions were evaluated. To correct for ME, an isotopic internal standard (IIS) method was developed, with the strengths and limitations of the approach discussed. This study provides a framework for applying SPME within complex sample systems where the influences of ME are inevitable, thus ensuring more accurate quantitation of analytes during biological and environmental analysis.