The Fornax cluster galaxies NGC 1399 and NGC 1404 are ideal for studying the effects of a cluster environment on globular cluster systems. Here we present new optical imaging of these two galaxies from both the Hubble Space Telescope's Wide Field and Planetary Camera 2 and the Cerro Tololo Inter-American Observatory's 1.5m telescope. The combination of both data sets provides unique insight on the spatial and colour distribution of globular clusters. From B-I colours, we find that both galaxies have a broad globular cluster metallicity distribution that is inconsistent with a single population. Two Gaussians provide a reasonable representation of the metallicity distribution in each galaxy. The metal-rich subpopulation is more centrally concentrated than the metal-poor one. We show that the radial metallicity gradient can be explained by the changing relative mix of the two globular cluster subpopulations. We derive globular cluster surface density profiles, and find that they are flatter (i.e. more extended) than the underlying starlight. The total number of globular clusters and specific frequency are calculated to be N = 5700 +/- 500, S_N = 11.5 +/- 1.0 for NGC 1399 and N = 725 +/- 145, S_N = 2.0 +/- 0.5 for NGC 1404. Our results are compared to the expectations of globular cluster formation scenarios.