Rapid detection of uremic toxins is crucial due to their severe health risks, including oxidative stress, inflammation, neurotoxicity, cardiovascular complications, and progression of chronic kidney disease. Surface-enhanced Raman spectroscopy (SERS) may provide sensitive, fast, and clinical-grade real-time monitoring of these toxins, enabling effective management with timely dialysis treatments. This study introduces a 3D-printed microchamber that integrates the fabrication of plasmonic metal nanoparticles for the in-flow detection of biological toxins and pharmaceutical drugs using SERS, making it ideal for on-site diagnostics in clinical settings. The microchamber supports quantitative and highly reproducible detection with liquid volumes under 100 μL, which is crucial for trace-level biomarker detection and minimizing cross-contamination. It employs a tunable solvent exchange method for the in situ synthesis of silver nanoparticles (AgNPs) on flexible PDMS or rigid Si wafer substrates, avoiding costly nanofabrication techniques. Ultralow detection limits were achieved for two model compounds and three pharmaceutical drugs: 10 −11 M for rhodamine 6G, 10 −7 M for adenine, and 10 −6 M for the pharmaceutical drugs. A total of 13 biological toxins, including three neurotransmitters, one neuromodulator, five amino acids, two polyamines, and two urea cycle metabolites, were detected with quantitative limits ranging from 10 −3 to 10 −6 M, all below permissible levels and aligning with physiological conditions. SERS detection within microchambers facilitates rapid on-site analysis, proving ideal for personalized health monitoring, point-of-care diagnostics, and environmental pollution assessment.