This paper aims to understand the hydrothermal sites near the Yonaguni Knoll IV in the Okinawa Trough, and to develop new techniques to study fluid flow patterns for hydrothermal systems and their impact on ore deposits on the seafloor. Hydraulic parameters are important for hydrothermal system studies, but in-situ measurements of fluid migration rates are difficult. Hydrothermal fluids can reach several hundred degrees Celsius, temperatures high enough to perturb hydrothermal fields and pore water migration patterns. Using in-situ temperature data as constraints, we model and synthesize 1D and 3D cylindrical hydrothermal models to fit the spatial variations of observed temperature fields. The 1D modeling uses Péclet number analysis along the conduit. We also construct a 3D cylindrical model to estimate the temperature and fluid velocity fields using a finite element software. All domains are set to be porous to allow the fluid to flow. The simulation is run until it reaches a semi steady-state solution, allowing both the temperature and velocity fields to stabilize. Results show the dimension of the thermal anomaly zone is likely controlled by advective heat transfer along the vent due to upward fluid flow. We estimate a Péclet number of −1.6, and the vertical ﬂuid ﬂow velocities at these sites are high, approximately 10-6 m/s, that is, about 100 m/year. This is a spatially averaged estimate over tens to hundreds of meters and does not take into account finer-scale venting, which may be very heterogeneous. The results of this work may help estimate the quantity of metal elements transported through pore fluid migration at modern hydrothermal sites.