This study demonstrated sampling biases of minnow traps in shallow, estuarine locations on the Eastern Shore of Virginia, USA. We exhaustively seined six shallow-water sites (including semi-permanent barrier island ponds, permanent mainland marsh ponds, tidal pools, and tidal rivulets) and compared these collection data to those obtained with minnow traps. The relative frequency of occurrence of fish species was significantly different between the two methods in all cases. Further comparison of the two techniques at ten additional sites representing a wide variety of habitat types and sizes suggested similar biases inherent to minnow traps. Specifically, minnow traps bias toward collection of a common marsh resident, the mummichog Fundulus heteroclitus, and bias against collection of several other resident species and juveniles of estuarine transient species. Minnow traps can be an effective collection technique for certain nekton species; however, specific biases inherent to the technique preclude their use as a method to accurately describe fish assemblages in shallow-water estuarine habitats.