Pitfall-trapping used in conjunction with drift-fence arrays is a common and effective means for detecting herpetofauna and small terrestrial mammals. A concern when using less-selective trapping methods is the impact of capture on target and non-target species. We compared capture and mortality rates of non-target species during a herpetofaunal study of temporary wetlands on forested lands in Mississippi, USA, March 2004–March 2006. We compared rates from pitfall traps, double-ended funnel traps, and pitfall traps combined with anti-predator wire exclusions along drift-fence arrays in 4 isolated upland and 6 floodplain ephemeral pools. We monitored traps daily for 23 5–10-day trap periods over a 2-year period. We captured 10 small mammal species (216 captures) on upland sites and 8 species (256 captures) on floodplain sites. Southern short-tailed shrews (Blarina carolinensis) and mice (Peromyscus spp.) accounted for 94% of total captures. Southern short-tailed shrews and mice suffered 76% and 52% mortality. Capture and mortality rates for small mammals were similar in un-excluded pitfall traps and excluded pitfall traps. Because of potential impact of pitfall-trapping on small mammals, we recommend researchers either alter trapping methods to address mortality in non-target species or work cooperatively using an integrated survey approach for both herpetofauna and small mammals. © 2014 The Wildlife Society.