RNA methylation is essential for appropriate assembly of ribonucleoprotein complexes. Dynamics of RNA methylation is thus important, but we lack quantitative methods to comprehensively assess it. We developed 13C-dynamods, an isotopic labelling approach using 13C-methyl-methionine, to quantify the turnover of base modifications in newly synthesized RNA, which is effective in distinguishing modifications in mRNAs from those in ncRNAs. This approach detected the presence of N6,N6-dimethyladenosine (m62A) in mRNA and tRNA in mammalian cells, and uncovered distinct kinetics of N-6-methyladenosine (m6A) and N-7-methylguanosine (m7G) in mRNA. Moreover, by assessing RNA metabolism during T-cell activation, we showed how methylation dynamics is coordinated with ribonucleotide biosynthesis. Finally, by quantification of methylation turnover and ribonucleoside abundance, we uncover the post-transcriptional lability of m6A in response to metabolic stress. Thus, 13C-dynamods enables studies of the origin, maintenance and biological regulation of RNA modifications under steady-state and non-stationary conditions.