This dataset comprises two Excel .csv files and three Excel .xlsx files containing all field data collected in 2018. Additionally, it includes four R-scripts utilized to generate the results presented in the manuscript. The data consists of morphometric measurements of harbor seal (Phoca vitulina vitulina) pups and young weaners during their time at Sealcentre Pieterburen in 2018. The objective of our study was to identify body measurements that serve as accurate age estimators for young harbor seals (up to three months old), with a focus on non-invasive techniques applicable in field conditions.