Invertebrate drift is a key process in riverine ecosystems controlling aquatic invertebrate distribution and availability to fish as prey. However, accurately quantifying drifting invertebrates of all sizes is difficult because the fine-mesh nets required to capture the smallest specimens clog easily, which reduces filtration efficiency and measurement accuracy. To address this problem, we developed a gas-powered pump system that delivers 20 m3/hour of river water through nested 80- and 750-μm-mesh nets suspended in the air. We compared 17 pumped samples with those obtained by adjacent, conventional deployment of a 250-μm drift net in a clear-water Alaskan river during both low and high flows. Our drift pump system sampled a geometric mean drift concentration of 467 invertebrates m−3 (maximum 5637 m-3) – eleven times the mean concentration of 42 m−3 estimated using the drift net. Invertebrates ≤ 3 mm long, primarily chironomids, comprised the entire difference between methods. Investigators for whom the drift of 0.5–3 mm invertebrates might be relevant (e.g., those applying foraging models for juvenile drift-feeding fishes) should consider using a pump or similar aerial filtration method to quantify small invertebrate drift, lest they underestimate it by an order of magnitude.