Fish biomass, species richness and composition were compared between upland streams draining two contrasting geological units (Pebas and Tsa) in Colombian Amazonia. Because Pebas sediments reportedly show higher levels of base concentrations than Tsa sediments, we expected that the fish communities from the Pebas streams would show highest biomass and species richness, and that the species composition would vary between the two upland systems. Eight forest streams were sampled in four locations, applying four daily sampling events. Tsa soil samples were comparatively sandy, whereas Pebas soil samples tended to be siltier, with higher levels of exchangeable acidity, Ca, Mg and total bases. Conductivity, concentrations of bases (Ca, Mg, K and Na), bicarbonates and temperature showed higher values in Pebas stream-water samples than in Tsa. In total, 7696 fish individuals were captured, belonging to eight orders, 28 families and 122 species. Pebas streams had 1.3 times more species than Tsa streams, and more than twice the total biomass. Species richness and biomass were highly correlated with conductivity and water concentrations of Mg and Na, and biomass alone with dissolved oxygen. Fish species composition differed significantly between the geological units. Species turnover was not related to distance between sampling locations.