The physical environment of natural waters influences biogeochemical processes to generate specific ecological niches, promoting biophysical interactions. Bacteria and phytoplankton communities can form spatial structures, such as layers and patches. The physical characteristics of these structures in lakes, particularly their vertical and horizontal variability are the focus of this PhD thesis. Using temperature microstructure measurements, we aim to characterize turbulent mixing within biological formations and their surroundings in lakes. We start in Lake Cadagno, where unusual bio-convectively-driven mixing takes place. Then we move to Lake Zurich where a thin layer of cyanobacteria persists throughout the stratified season. Finally, we study the thermocline of Lake Geneva, a large and more energetic system, where basin-scale processes are expected to induce lateral variability of algae. While the first two interactions concern vertical structures, we use an autonomous underwater glider, equipped with a turbulence package, to explore lateral variability in this large lake. Bioconvection observed in Lake Cadagno offered a unique environment to analyze the role of microorganism in shaping the water column they inhabit. Within the stratified water column, a highly concentrated layer of heavy, motile and photoautotrophic sulfur bacteria Chromatium okenii migrates upward to form a subsurface convective mixed layer. Field measurements revealed that the mixed layer persists throughout the diel cycle, maintaining a virtually unchanged structure. Direct estimates of turbulent diffusion indicate that without active convective turbulence, the mixed layer would be smoothed in ≈2.5 hours. As this time-scale is much shorter than a night and in principle C. okenii need light, the nighttime mixed layer is not expected. Using intensive and high-resolution measurements throughout two diel cycles, we provide proof that bioconvection occurs also at night and is responsible for the mixed layer persistence. The second interaction was the thin layer of cyanobacteria Planktothrix rubescens forming every spring in the thermocline of Lake Zurich. In this zone, our measurements revealed only tiny overturns, resulting in negligible vertical exchange. This strong stratification inhibits mixing and provides a remarkably stable environment for the P. rubescens thin layer, explaining its persistence. Finally, in Lake Geneva, we first concentrated efforts in the validation of glider-based turbulence estimations, possibly the first of their kind in a large-lake. Although weak turbulence and strong stratification hinder the applicability of state of the art procedures, we demonstrate that our measurements capture the expected variance and spectral shape. We explore the data from repeated transects to assess lateral variability of chlorophyll-a patches. This thesis documents in an exemplary way how vertical turbulent processes interact with bacteria and phytoplankton layers in lakes. Regarding lateral variability, the results presented are a first step for future in-situ studies of phytoplankton patches affected by turbulence and transport processes.