Researches on ichthyoplankton seems to be an important tool to identification of spawning areas and periods for freshwater fish. Ichthyoplankton was sampled monthly in the headwaters of the Cuiabá River, upper Paraguay River basin, (Mato Grosso State, Brazil), and in four of its tributaries, between November 2007 and March 2008, to evaluate the spatial and temporal distribution of fish eggs and larvae and the influence of regional and local variables on their distribution. In total, 22,067 eggs and 1,045 larvae were collected. A significant negative correlation was found between egg density and the variables of river level and flow volume. Larval density was not significantly correlated with any of the regional variables. The egg and larval densities were significantly higher at the sampling sites in the main river. The highest densities were found in environments with greater river widths, intermediate depths and lowest values of dissolved oxygen, electrical conductivity, and transparency. Anostomidae, Zungaro zungaro, Bryconamericus spp., Pimelodus spp., Pimelodidae, Auchenipteridae, and Siluriformes were the most abundant groups of larvae, and were observed at the sampling sites in the main river. The study site is an important spawning area for migratory and, non-migratory fish species, and highlight the importance of the main river to the reproductive event, by the influence of local variables transparency and river width, which in turn maybe temporally influenced by the river level.