Assessing automated gap imputation of regional scale groundwater level data sets with typical gap patterns

•A new approach to assess imputation performance considering gap patterns.•The approach mimics gaps found in regional scale groundwater level data set.•The MissForest algorithm outperforms imputePCA and linear interpolation in infilling daily groundwater hydrographs.•MissForest accurately imputes continuous gaps at the beginning or end of hydrographs, and around peaks.•However, hydrographs having unseen extremes (droughts) or water abstraction impacts are challenging to impute.