Fish larvae in riverine environments often disperse (e.g., drift) from areas of egg deposition at the time of hatch. Several components of drift can be important in terms of survival including timing, distribution in the water column, and body size. The longitudinal and cross-sectional aspects of larval lake sturgeon (Acipenser fulvescens) drift from upstream spawning sites have received considerable study. However, the vertical distribution of larval lake sturgeon in the water column has not been comprehensively evaluated with respect to river size, water depth, the size of larvae in drift over the entire drift period, and the effectiveness of traditional sampling gear (D-frame nets) designed to collect larvae along the river bottom. In 2013, we sampled larval lake sturgeon drifting from upstream spawning sites in the Menominee and Oconto Rivers (Wisconsin, USA) using traditional D-frame nets and custom fabricated sampling nets that vertically partitioned the water column. Drifting larval lake sturgeon were observed from the river bottom to the top of the water column in both systems. Vertical net section was a significant predictor of total larval catch with the highest catch occurring in nets towards the center of the water column but was dependent on net location within the rivers’ cross section and downstream distance from spawning locations. 42% of larvae captured across both rivers were outside of the sampling capability of the traditional D-frame nets (i.e., fish would have drifted over the top). Studies seeking to describe larval production for lake sturgeon, as well as other fish species that exhibit drift in larval dispersal, need to consider a balance between net design and sampling the vertical/cross sectional profiles of rivers. Size-based vertical drift may also have consequences for studies seeking to estimate genetic parameters (e.g., diversity and parentage).