We quantified nesting activity and incidence of nest flooding in a population of the Magdalena River turtle (Podocnemis lewyana), which inhabits the climatic equator in northern Colombia, during two dry seasons when beaches formed (“verano”—December to March—and “veranillo”—July and August). Nesting activity was concentrated in the verano period, despite the presence of suitable nesting habitat in both dry season periods. More than half of all nests were harvested by local people, and 42.5% of the nests in both dry seasons that survived harvest were subsequently lost to flooding due to rises in the river to approximately a 4.15 m level. We used this value as a threshold value for the appearance of beaches and inspected a 44-year data base on river levels in this area. The verano and veranillo nesting periods did not differ in terms of opportunities for successful nesting, but there was evidence that the veranillo nesting season has increased significantly in duration in recent years, as well as experienced fewer flooding events. It is not clear why nesting each year is principally concentrated in the verano nesting season, but the evidence that this section of the Magdalena River is drying more in recent years during veranillo may entail a new threat to this population if it implies that non-nesting habitat (adjacent wetlands and channels) might eventually disappear.