Context Water pumps fitted with filtering screens are effective for delivering water to floodplain environments and excluding large-bodied exotic fish; yet, the benefits to wetland fish and anurans are unknown. Aims To quantify fish and tadpole responses to refilling wetlands with water pumps fitted with large-mesh screens following drawdown v. overland reconnections in the mid-Murrumbidgee region of New South Wales. Methods Frog and fish communities were compared between wetlands under managed inundation and overland reconnections by using PERMANOVA, and non-metric multidimensional scaling was used to evaluate community divergence between watering strategies. Classification and regression trees were used to identify thresholds in explanatory variables and predicted threshold responses in fish and tadpole abundance. Key results Fish and tadpole communities differed in relation to watering strategies. Managed inundation resulted in a higher abundance of tadpole species and one native fish, whereas overland reconnections resulted in a high abundance of exotic fish species and fewer tadpoles. Water depth was a driver of tadpole abundance in two species, including the threatened southern bell frog (Litoria raniformis). Conclusions and implications Using filtered pumps with large-mesh screens to deliver water to wetlands of high conservation value may be an effective strategy for reducing large-bodied exotic fish and enhancing frog and fish populations in regulated floodplain systems.