Described are computer-based methods and apparatuses, including computer program products, for dynamic deduplication. Data is processed using an algorithm that deduplicates the data based on a first set of parameters. A first moving average of a first deduplication performance metric is calculated for the algorithm over a time period. A second moving average of a second deduplication performance metric is calculated for the algorithm over the time period. It is determined that the first moving average satisfies a first criterion, the second moving average satisfies a second criterion, or both. The algorithm is reconfigured based on a second set of parameters to deduplicate data.