From the diffusional behavior of nanoparticles in heterogeneous hydrogels, quantitative information about sub-micron structural features of the polymer matrix can be derived. Pulsed-gradient spin-echo NMR is often the method of choice, because it measures diffusion of the whole ensemble of nanoparticles. However, in 1H diffusion-ordered spectroscopy (DOSY), low-intensity nanoparticle signals have to be separated from a highly protonated background. To circumvent this, we prepared 19F labeled, PEGylated, water-soluble dendritic nanoparticles with a 19F loading of ~7 wt% to enable background free 19F DOSY experiments. 19F nanoparticle diffusometry was benchmarked against 1H diffusion-T2 correlation spectroscopy (DRCOSY), which has a stronger signal separation potential than the commonly used 1H DOSY experiment. We used bootstrap data resampling to estimate confidence intervals and stabilize 2D-Laplace inversion of DRCOSY data with high noise levels and artifacts, allowing quantitative diffusometry even at low magnetic field strengths (30 MHz). The employed methods offer significant advantages in terms of sensitivity and selectivity.