Seed germination is a developmental progression from complete metabolic dormancy to a highly active, growing seedling. Extensive studies of hormonal, transcriptional and translational control during germination have been conducted. However, the role of epigenetic regulation in germination is not yet understood. We present here an integrated high-resolution RNA-seq, small RNA-seq and MethylC-seq analysis over 10 time points in Arabidopsis thaliana; from fresh seed, through ripened seed then dark stratification, to germination and post-germination (48 h post-stratification). It reveals extensive transcriptomic and epigenetic transformations associated with seed germination. Our analyses identify unannotated transcripts that are expressed transiently over the time-series. We model dynamic transcription factor networks governing germination by integration of our transcriptome time-series data with public transcription factor-gene interaction data. Expression of both miRNA and siRNA clusters changed significantly during germination, particularly between the seed and the post-germinative seedling. These correlated with significant changes in gene expression and large-scale demethylation observed towards the end of germination and post-germination. This suggests epigenetic regulation has a temporally-specific role in the seed-to-seedling transition.