Diseases of the central nervous system (CNS) manifest through a complex, dynamic network of intercellular communication. Glioblastoma (GBM), the most common and aggressive primary brain tumor, is emblematic of this complexity, with its rapid progression and dismal prognosis measured in months rather than years. GBM's biology is driven by intricate signaling molecule exchanges between neoplastic and stromal cells, underpinning aggressive disease progression. Here, we describe a detailed cerebral open-flow microperfusion (cOFM) protocol in GBM mouse models, enabling real-time longitudinal monitoring of tumor microenvironment dynamics within the interstitial fluid (ISF). Our approach describes the implantation of durable guide cannula head-mounts, their use for intracerebral glioma engraftment directly through the guide, and the collection of high-fidelity cOFM samples for metabolomic and proteomic LC-MS analyses. Crucially, cOFM overcomes the molecular size limitations of traditional microdialysis. Beyond GBM, cOFM methodology promises transformative insights into a spectrum of CNS disorders, including neurodegenerative, epileptic, and neuropsychiatric conditions, through its capacity to provide etiological and treatment-responsive biomarkers within their respective animal models.