Eleotrid fish (gudgeons) commonly dominate the small-fish fauna throughout much of the Indo-Pacific region. Eleotrids frequently occupy habitats comprised of dense emergent macrophytes, making estimation of fish abundance difficult. In this study, the suitability of unbaited fish traps to measure carp gudgeon (Hypseleotris spp.) abundance in giant rush habitats was studied in a River Murray floodplain billabong using depletion trapping. Traps were repeatedly set at ten locations within giant rush beds over a two-day period. There was no significant variation in carp gudgeon catch rate over time within locations, but variation between locations was significant. It was not possible to deplete fish from any location over two days of trapping, suggesting rapid replacement of trapped fish in sampled locations. Patch specific variation in the gudgeon catch rate among different traps in macrophyte beds may reflect small-scale variation in habitat quality.