A compact, inexpensive capillary electrophoresis instrument was developed for monitoring metal ions and evaluated for Zn(II) in remote contaminated locations in western Tasmania, Australia. The portable instrument, measuring 21 cm x 10 cm x 7 cm, was powered from the USB port of a laptop computer and built from off-the-shelf components costing ∼$1200 USD. Electrophoretic separations were conducted using a fused silica capillary (10–50 µm I.D.), applying 8.5 kV over capillaries ranging from 25 cm to 40 cm in length. The capillary inlet was connected with an electrically grounded cross-piece as flow-through injection interface. Automated fluidic management was achieved by controlling four mini peristaltic pumps and a solenoid valve. Detection was realised using a purpose-built visible LED absorption detector, optimised for the detection of Co(II), Cu(II) and Zn(II) after complexation with 4-(2-Pyridylazo) resorcinol (PAR). Limits of detection of sub-µM were obtained. The instrument was tested for continuous operation in the laboratory for up to 3 months, and relative standard deviations of <5.4% were found over 945 consecutive injections. In the field, the system was able to measure 106 samples within 11 h, the time it can be powered from the laptop computer. As Field measurement of Zn(II) in western Tasmania was demonstrated to show capability for on-site metal testing.