Few long-term demographic studies have been conducted on freshwater turtles of South America, despite the need for this type of inquiry to investigate natural variation and strengthen conservation efforts for these species. In this study, we examined the variation in demography of the Chocoan River Turtle (Rhinoclemmys nasuta) based on a population from an island locality in the Colombian Pacific region between 2005 and 2017. We calculated survival, recapture, and transition probabilities, and the effects of stream substrate and El Niño–Southern Oscillation (ENSO) phases (El Niño, Neutral, La Niña) on these variables using a multi-state model. We found differences in survival probabilities between ENSO phases, likely as a consequence of an increase in flood events. In addition, we found support for survival being greater in muddy streams than rocky streams, possibly because it is easier to escape or hide in mud substrates. Recapture probabilities varied by life stages; differences in the probability of recapture between size classes were associated with the high fidelity to territories by adults. The present increases in frequency and severity of El Niño and La Niña may exacerbate the consequences of climatic regimes on natural populations of turtles by increasing the mortality caused by drastic phenomena such as floods.