Arboreal lizards, especially species that inhabit flood-prone environments, have been poorly surveyed worldwide. We examined spatiotemporal patterns in arboreal lizard abundance and factors driving detection rates in floodplain environments using artificial bark covers, a non-destructive and cost-effective survey method. In total, 112 flexible, closed-cell foam bark covers were installed on eucalypt trees in 13 wetlands in the Murrumbidgee River floodplain of southern New South Wales, Australia, stratified by two inundation frequency treatments. Of four arboreal lizard species detected, the southern marbled gecko (Christinus marmoratus) (n = 41) and the tree dtella (Gehyra versicolor) (n = 8) were restricted to the mid-Murrumbidgee region, whereas the crevice skink (Egernia striolata) (n = 19) was restricted to the lower-Murrumbidgee region and did not co-occur with either gecko species. Mean detection rates of lizard species did not differ between frequently and infrequently inundated treatments but their abundance beneath covers varied significantly by month. For all detected lizard species, the presence/absence of the arachnid Holconia murrayensis represented a significant variable in explaining lizard occurrence patterns, particularly that of C. marmoratus. Artificial bark covers are a useful survey method for collecting distribution, abundance, and occupancy data on floodplain reptiles, although detection rates can be affected by the month, predator–prey interactions, and survey effort. Adopting passive, non-destructive reptile survey methods would greatly improve our knowledge of species’ distributions and abundance patterns in vegetation communities subject to disturbance events.