A variable checkpoint mechanism in a streams manager checkpoints a streaming application based on periodic time periods for checkpoints. The variable checkpoint mechanism can take a checkpoint early before a periodic time period ends or late after the periodic time period ends based on predicted size of one or more tuple windows in the streaming application. The time for taking the checkpoint can be selected based on multiple checkpoint timing criteria, which include storage requirement for the checkpoint and predicted backpressure in the flow graph. In this manner the checkpoint timing of the variable checkpoint mechanism can be adjusted real-time to minimize the negative impact of checkpointing on the performance of the streaming application.