When animals swim in aquatic habitats, the water through which they move is usually flowing. Therefore, an important part of understanding the physics of how animals swim in nature is determining how they interact with the fluctuating turbulent water currents in their environment. We addressed this issue using microscopic larvae of invertebrates in "fouling communities" growing on docks and ships to ask how swimming affects the transport of larvae between moving water and surfaces from which they disperse and onto which they recruit. Field measurements of the motion of water over fouling communities were used to design realistic turbulent wavy flow in a laboratory wave-flume over early-stage fouling communities. Fine-scale measurements of rapidly-varying water-velocity fields were made using particle-image velocimetry, and of dye-concentration fields (analog for chemical cues from the substratum) were made using planar laser-induced fluorescence. We used individual-based models of larvae that were swimming, passively sinking, passively rising, or were passive and neutrally buoyant to determine how their trajectories were affected by their motion through the water, rotation by local shear, and transport by ambient flow. Swimmers moved up and down in the turbulent flow more than did neutrally buoyant larvae. Although more of the passive sinkers landed on substrata below them, and more passive risers on surfaces above, swimming was the best strategy for landing on surfaces if their location was not predictable (as is true for fouling communities). When larvae moved within 5 mm of surfaces below them, passive sinkers and neutrally-buoyant larvae landed on the substratum, whereas many of the swimmers were carried away, suggesting that settling larvae should stop swimming as they near a surface. Swimming and passively-rising larvae were best at escaping from a surface below them, as precompetent larvae must do to disperse away. Velocities, vorticities, and odor-concentrations encountered by larvae fluctuated rapidly, with peaks much higher than mean values. Encounters with concentrations of odor or with vorticities above threshold increased as larvae neared the substratum. Although microscopic organisms swim slowly, their locomotory behavior can affect where they are transported by the movement of ambient water as well as the signals they encounter when they move within a few centimeters of surfaces.