The location of estuarine organisms varies based on geophysical cycles and environmental conditions, which can strongly bias understanding of organism abundance and distribution. In the San Francisco Estuary, California, extensive monitoring surveys have provided insight into the life history and ecology of certain commercially important or legislatively protected fish species. However, there remains substantial uncertainty in factors influencing the vertical and lateral distributions of many other nekton species in the San Francisco Estuary, including longfin smelt Spirinchus thaleichthys, for whom such distributional information may highly influence interpretation of existing data. We carried out paired sampling using surface and demersal gears to address three questions: (1) Does diel phase influence the vertical position of nekton (e.g., surface versus demersal)? (2) Do environmental conditions, specifically turbidity, influence the vertical and lateral positions of nekton (e.g., center channel versus peripheral shoal)? (3) Does tidal variability influence vertical and lateral distributions of nekton? We documented variability in sampled nekton densities across diel phase (day/night), vertical position (surface/bottom), and lateral position (channel/shoal). Tidal phase and turbidity concentration influenced vertical and lateral distributions for some species at certain locations. Although infrequently encountered, we documented associations of longfin smelt with the lower water column and shoal habitats, with some evidence for upward vertical shifts in low light conditions brought about by nightfall or elevated turbidity. Observed habitat associations provide insight into how interacting geophysical and environmental factors may influence the distribution of nekton and thus the vulnerability of individual species to detection by sampling gears.