This dataset includes model configurations, scripts and outputs to process and recreate the outputs from Ladwig et al. (2021): Long-term Change in Metabolism Phenology across North-Temperate Lakes. The provided scripts will process the input data from various sources, as well as recreate the figures from the manuscript. Further, all output data from the metabolism models of Allequash, Big Muskellunge, Crystal, Fish, Mendota, Monona, Sparkling and Trout are included.