The profiling of the most lethal paralytic shellfish poisoning toxins (PSTs) in freshwater has increased the need to establish an alternative analytical method with high sensitivity and resolution. In this paper, a coupling technique of field-amplified sample injection (FASI) and CE with end-column amperometric detection (CE-AD) was developed to improve the detection sensitivity and separation of PSTs by electrokinetically injecting a water plug of analytes to the capillary filled with a high-conductivity BGE. Parameters affecting FASI and CE process were carefully adjusted to achieve the highest response and resolution. Separation selectivity for PSTs, especially for the analogues and epimers, was greatly enhanced by using 40 mM Britton-Robinson buffer (pH 9.5) as BGE, which altered the EOF and mobility of the analytes that interacted with polyborate ions. Satisfactory linear relationship between peak current and concentration of toxins were gained over a wide range of 1.95-254 mu g/L. The detection limits (S/N = 3) for five PSTs ranged from 0.63 to 3.11 mu g/L, which are below the health alert level in drinking water. In comparison with the up-to-date reporting chromatographic methods, the FASI-CE-AD method was simple, low-cost, selective, and sensitive enough for direct quantification of PSTs at very low levels, implying a potential for screening and monitoring of PSTs in surface waters.