Species-specific welfare indicators are important in promoting positive welfare for zoo animals. Reptiles are a notoriously understudied group in regards to behavior, welfare needs, and husbandry requirements. Using opportunistically obtained samples, we evaluated how blood lactate is affected by variation in manual capture and restraint in crocodilians. Lactate is an indicator of anerobic metabolism in reptiles. It offers a relatively simple and indirect way to assess physiological stress. Determining the best way to reduce struggling during capture and associated stress is of great importance to these species’ overall welfare. Blood samples (N = 53) were collected from 10 different species of crocodilians. It was found that age class was a significant predictor variable of lactate levels after capture, and longer handling time seemed to cause an increase in lactate. Finally, draining enclosure pools for a small number of the captures was associated with higher lactate levels compared to other capture factors that were recorded. This study showed that welfare of captive crocodilians could be improved by shortening the duration of physical restraint events when possible. Developing objective measures of welfare and establishing baseline recommendations for care and handling of crocodilians will ultimately promote and improve their wellbeing, along with that of other understudied reptiles in zoos.