The precipitation and diabatic heating resulting from moist convection make it a key component of the atmospheric water budget in the tropics. With convective parameterization being a known source of uncertainty in global models, convection-permitting (CP) models are increasingly being used to improve understanding of regional climate. Here, a new 10-yr CP simulation is used to study the characteristics of rainfall and atmospheric water budget for East Africa and the Lake Victoria basin. The explicit representation of convection leads to a widespread improvement in the intensities and diurnal cycle of rainfall when compared with a parameterized simulation. Differences in large-scale moisture fluxes lead to a shift in the mean rainfall pattern from the Congo to Lake Victoria basin in the CP simulation—highlighting the important connection between local changes in the representation of convection and larger-scale dynamics and rainfall. Stronger lake–land contrasts in buoyancy in the CP model lead to a stronger nocturnal land breeze over Lake Victoria, increasing evaporation and moisture flux convergence (MFC), and likely unrealistically high rainfall. However, for the mountains east of the lake, the CP model produces a diurnal rainfall cycle much more similar to satellite estimates, which is related to differences in the timing of MFC. Results here demonstrate that, while care is needed regarding lake forcings, a CP approach offers a more realistic representation of several rainfall characteristics through a more physically based realization of the atmospheric dynamics around the complex topography of East Africa.