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Abstract The meroplanktonic larvae of many invertebrate and vertebrate species rely on physical transport to move them across the shelf to their adult habitats. One potential mechanism for cross‐shore larval transport is Stokes drift in internal waves. Here, we develop theory to quantify the Stokes velocities of neutrally buoyant and depth‐keeping organisms in linear internal waves in shallow water. We apply the analyses to theoretical and measured internal wave fields, and compare results with a numerical model. Near the surface and bottom boundaries, both neutrally buoyant and depth‐keeping organisms were transported in the direction of the wave's phase propagation. However, neutrally buoyant organisms were transported in the opposite direction of the wave's phase at mid depths, while depth‐keeping organisms had zero net transport there. Weakly depth‐keeping organisms had Stokes drifts between the perfectly depth‐keeping and neutrally buoyant organisms. For reasonable wave amplitudes and phase speeds, organisms would experience horizontal Stokes speeds of several centimeters per second—or a few kilometers per day in a constant wave field. With onshore‐polarized internal waves, Stokes drift in internal waves presents a predictable mechanism for onshore transport of meroplanktonic larvae and other organisms near the surface, and offshore transport at mid depths. 

Abstract Coastal physical processes are essential for the cross‐shore transport of meroplanktonic larvae to their benthic adult habitats. To investigate these processes, we released a swarm of novel, trackable, subsurface vehicles, the Mini‐Autonomous Underwater Explorers (M‐AUEs), which we programmed to mimic larval depth‐keeping behavior. The M‐AUE swarm measured a sudden net onshore transport of 30–70 m over 15–20 min, which we investigated in detail. Here, we describe a novel transport mechanism of depth‐keeping plankton revealed by these observations. In situ measurements and models showed that, as a weakly nonlinear internal wave propagated through the swarm, it deformed surface‐intensified, along‐isopycnal background velocities downward, accelerating depth‐keeping organisms onshore. These higher velocities increased both the depth‐keepers' residence time in the wave and total cross‐shore displacement, leading to wave‐induced transports twice those of fully Lagrangian organisms and four times those associated with the unperturbed background currents. Our analyses also show that integrating velocity time series from virtual larvae or mimics moving with the flow yields both larger and more accurate transport estimates than integrating velocity time series obtained at a point (Eulerian). The increased cross‐shore transport of organisms capable of vertical swimming in this wave/background‐current system is mathematically analogous to the increase in onshore transport associated with horizontal swimming in highly nonlinear internal waves. However, the mechanism described here requires much weaker swimming speeds (mm s⁻¹vs. cm s⁻¹) to achieve significant onshore transports, and meroplanktonic larvae only need to orient themselves vertically, not horizontally.