We report on the measurement of the 2s-3s transition frequencies in the stable lithium isotopes and 2s-2p isotope shift measurements of 7,9,10,11Be, using a femtosecond frequency comb. For the beryllium isotopes, we extract the changes in the mean-square nuclear charge radius along the isotope chain by comparison with high-precision atomic mass shift calculations. The 2s-3s transition frequency is compared with theoretical calculations, and possibilities to extract an absolute value for the nuclear charge radius of lithium isotopes are discussed.