The intricate interplay of physical, chemical, and biological processes in fjord ecosystems fosters primary production and ecological diversity. Pinpointing specific outcomes, such as triggers for harmful algal blooms (HABs), a severe and still unresolved problem affecting coastal activities, is challenging due to the diverse spatial and temporal scales involved. To address this, our study focuses on identifying repeatable patterns critical for plankton dynamics (including HAB species), particularly the diurnal cycle. In December 2021, we conducted comprehensive fieldwork in a fjord in northern Chilean Patagonia to capture a full 24-hour diurnal cycle of these processes. Our findings revealed distinct patterns: thin layers of phytoplankton and zooplankton formed during the day but dissipated at night due to predator-prey interactions and increased vertical mixing, likely influenced by swimming macrozooplankton. A generalized linear model analysis revealed that vertical shear was a significant component, particularly at nighttime, contributing to chlorophyll-a dispersion, even with zooplankton migration to the surface layer. Our interdisciplinary approach highlights the importance of understanding these interactions for predicting and mitigating water quality issues, including harmful algal blooms.