Microbes play a primary role in aquatic ecosystems and biogeochemical cycles. Patchiness is a critical component of these activities, influencing biological productivity, nutrient cycling and dynamics across trophic levels. Incorporating spatial dynamics into microbial models is a long-standing challenge, particularly where small-scale turbulence is involved. Here, we combine a realistic simulation of turbulence with an individual-based microbial model to test the key hypothesis that the coupling of motility and turbulence drives intense microscale patchiness. We find that such patchiness is depth-structured and requires high motility: Near the fluid surface, strong convective turbulence overpowers motility, homogenising motile and non-motile microbes equally. In deeper, thermocline-like conditions, highly motile microbes are up to 1.6-fold more patch-concentrated than non-motile microbes. Our results demonstrate that the delicate balance of turbulence and motility that triggers micro-scale patchiness is not a ubiquitous consequence of motility, and that the intensity of such patchiness in real-world conditions is modest.