99Tc is an artificial beta emitter widely used in nuclear medicine for diagnostic tests. A fully automated and rapid system for 99Tc monitoring is introduced with the aim to improve hospital residues management. This system can also be helpful for controlling urban wastewater. Figures of merit similar to those obtained with liquid scintillation counting were achieved by exploiting a simple, economic, and portable system with spectrophotometric detection. The combination of flow analysis techniques, i.e., lab-on-valve (LOV) and multisyringe flow injection analysis (MSFIA), with a selective resin ((weak base extraction chromatographic (WBEC) resin) enables the analysis to be performed in a short time, achieving high selectivity and sensitivity levels. After elution with NH4OH (3 mol·L-1), 99Tc is derivatized with 1,5-diphenylcarbohydrazide (DPC) and finally detected by a miniaturized fiber optic CCD spectrophotometer at 520 nm, exploiting a long path-length liquid waveguide capillary cell (LWCC) of 100 cm path length. The proposed method was optimized by experimental design, achieving a limit of detection (LOD) of 4 ng of 99Tc (2.5 Bq), a reproducibility of 6%, and a resin durability of 78 injections. The microcolumn allows one to preconcentrate up to 100 mL of sample without deterioration of the analytical signal. The automated system was successfully applied to hospital residues and urban wastewater, and the attained recoveries were between 90% and 110%.