Using a before-after study design in a stable, largely undisturbed pond habitat and a dataset spanning 33 years, we document and describe the decline of native Sonora mud turtles (Kinosternon sonoriense) after the introduction of non-native pond sliders (Trachemys scripta). The Sonora mud turtle population in Montezuma Well in central Arizona, USA, declined to less than 25% of previous numbers, from 372 ± 64 in 1983 to 80 ± 21 in 2011. We trapped and removed the non-native turtles between 2007 and 2012 and after removal of the non-natives, the Sonora mud turtle population increased to 139 ± 34 in 2015. The native turtles also significantly increased basking activity after removal of the non-natives, paralleling results of small-scale mesocosm studies showing that pond sliders negatively affect basking rates of native turtle species. Reproductive rates of female Sonora mud turtles (numbers of females with eggs) were lower during the period of peak non-native turtle abundance, and increased after removal of the non-native turtles. We hypothesize that the reduction in effective reproductive rate links interference competition (reflected in reduced basking rates) to the long-term decline of the native mud turtles. Results from the undisturbed natural system of Montezuma Well provide new insights on the overall occurrence, magnitude, and mechanisms of negative effects of introduced pond sliders on native turtle species. Sonora mud turtles are very different in their morphology, behavior, and ecology from pond sliders and from native turtles in other studies, suggesting that impacts of non-native pond sliders are more pervasive than previously thought.