Shallow-water hydrothermal vents are extreme environments that share many characteristics with their deep-sea analogs. However, despite ease of access, much less is known about the geochemical dynamics of these ecosystems. Here, we report on the spatial and temporal geochemical dynamics of a shallow-water vent system at Paleochori Bay, Milos Island, Greece. Our multi-analyte voltammetric profiles of dissolved O2 and hydrothermal tracers (e.g. Fe2 +, FeSaq, Mn2 +) on sediment cores taken along a transection in hydrothermally affected sediments indicate three different areas: the central vent area (highest temperature) with a deeper penetration of oxygen into the sediment, and a lack of dissolved Fe2 + and Mn2 +; a middle area (0.5 m away) rich in dissolved Fe2 + and Mn2 + (exceeding 2 mM) and high free sulfide with potential for microbial sulfide oxidation as suggested by the presence of white mats at the sediment surface; and, finally, an outer rim area (1–1.5 m away) with lower concentrations of Fe2 + and Mn2 + and higher signals of FeSaq, indicating an aged hydrothermal fluid contribution. In addition, high-frequency temperature series and continuous in situ H2S measurements with voltammetric sensors over a 6-day time period at a distance 0.5 m away from the vent center showed substantial variability in temperature (31.6 to 46.4 °C) and total sulfide (488 to 1329 μM) in the upper sediment layer. The analysis of these data suggests that tidal and wind forcing, and abrupt geodynamic events generate intermittent mixing conditions lasting for several hours to days. Despite substantial variability, the concentration of sulfide available for chemoautotrophic microbes remained high. However, the availability of electron acceptors originating from seawater might be more intermittent, which in turn has an effect on the reestablishment of the white mats after wave-induced disturbances. Our results emphasize the importance of transient events in the development of chemoautotrophic communities in the hydrothermally influenced sediments of Paleochori Bay.