The importance of aquatic arthropods in the processing of organic matter in fluvial systems is well known, but this topic has been poorly studied in Neotropical rivers. In this research, we studied the composition of functional feeding groups (FFGs) associated with differences in elevation in a tropical river in northern Colombia during the wet and dry seasons. Between 2008 and 2013, we collected benthic arthropods at 3 sites located in the upper (San Lorenzo), intermediate (La Victoria) and lower (Puerto Mosquito) sections of the Gaira River. We found some differences in the gut contents and FFGs of the animals from different sites and between the climatic seasons. The dominant food source at all the sites and during both seasons was fine particulate organic matter (FPOM). At La Victoria, the genera Leptonema, Smicridea and Phylloicus (all belonging to Trichoptera) presented significant differences in the consumption of coarse particulate organic matter (CPOM) between the rainy and dry seasons (p < 0.05). At San Lorenzo, Leptonema had the highest animal tissue consumption value (p < 0.05). A discriminant function analysis based on gut contents suggested that some taxa may have been assigned to the wrong FFGs. We concluded that the diets of the aquatic arthropods in our study tended to present high trophic plasticity. Consequently, our results suggest that Neotropical rivers need to be re-evaluated in terms of traditionally established FFGs, which heretofore have been based on information from other regions of the world, producing incorrect assessments of aquatic systems.