A comparative investigation of the isotope effect in multi-scale anomalous transport phenomena is performed both experimentally by highly localized turbulence diagnostics in comparable hydrogen and deuterium FT-2 tokamak discharges and theoretically with the help of global gyrokinetic modeling. Substantial excess of the geodesic acoustic mode (GAM) amplitude, radial wavelength and correlation length in a wide spatial region of deuterium discharge resulting in stronger modulation of drift-wave turbulence level is demonstrated by both approaches. A larger turbulence radial correlation length is found at LFS in D-discharge in experiment and a stronger modulation of gyrokinetic particles and energy fluxes is shown there by the gyrokinetic code. The gyrokinetic modeling demonstrated comparable levels of drift wave density and electric field fluctuations in hydrogen and deuterium discharges. Nevertheless, the mean value of the ion energy and particle anomalous flux provided by modeling shows the systematic isotope effect at all radii.