Spatio-temporally variable information on total vegetation cover is highly relevant to water quality and land management in river catchments adjacent to the Great Barrier Reef, Australia. A time series of the global Moderate Resolution Imaging Spectroradiometer (MODIS) Fraction of Photosynthetically Active Radiation (FPAR; 2000-2006) and its underlying biome classification (MOD12Q1) were compared to national land cover and regional, remotely sensed products in the dry-tropical Burdekin River. The MOD12Q1 showed reasonable agreement with a classification of major vegetation groups for 94% of the study area. We then compared dry-seasonal, quality controlled MODIS FPAR observations to (i) Landsat-based woody foliage projective cover (wFPC) (2004) and (ii) MODIS bare ground index (BGI) observations (2001-2003). Statistical analysis of the MODIS FPAR revealed a significant sensitivity to Landsat wFPC-based Vegetation Structural Categories (VSC) and VSC-specific temporal variability over the 2004 dry season. The MODIS FPAR relation to 20 coinciding MODIS BGI dry-seasonal observations was significant (ρ < 0.001) for homogeneous areas of low wFPC. Our results show that the global MODIS FPAR can be used to identify VSC, represent VSC-specific variability of PAR absorption, and indicate that the amount, structure, and optical properties of green and non-green vegetation components contribute to the MODIS FPAR signal.