Quantitative comparisons between benthic and hyporheic invertebrate communities are crucial for understanding the biological functions of the hyporheic zone, such as storage, migrations, and exchanges of invertebrates with the surface stream. Such comparisons are still hampered by the use of different techniques adapted to each habitat (benthic versus hyporheic). This work combines two different techniques for sampling the upper layers of bed sediments (0–15 cm): the semiquantitative “Bou-Rouch” pump classically used to sample the hyporheic zone (>15 cm), and the quantitative Hess sampler commonly used to sample the benthic zone (≤15 cm), in order to evaluate the quantitative efficiency of the pump in this 0–15 cm zone. First, a Bou-Rouch sample (BR) was taken within the cylinder of a Hess inserted within the streambed, then a second sample (benthic complement, BC) was collected within the Hess after removing the pump, in order to catch all invertebrates not extracted with the pump. The BR samples collected on average 14.5% of the total abundance and about 50% of the actual richness. The large range of variation indicates that the combination of the two techniques is not valid for a quantitative evaluation of benthic communities. Contrary to expectations, the pump did not collect more interstitial and groundwater invertebrates and no differences in faunal composition between upstream and downstream riffle positions were observed. Our results do not question the use of the BR technique under standard conditions i.e., when sampling the hyporheic zone, but underline how it is crucial to know its quantitative limits.