We present 2-D numerical simulations of two phase flow in seafloor hydrothermal systems using the finite control volume numerical scheme FISHES. The FISHES code solves the coupled non-linear equations for mass, momentum, energy, and salt conservation in a NaCl-H2O fluid to model the seafloor hydrothermal processes. These simulations use homogeneous box geometries at a fixed seafloor pressure of 25 MPa with constant bottom temperature boundary conditions that represent a sub-axial magma chamber to explore the effects of permeability, maximum bottom temperature and system depth on the evolution of vent fluid temperature and salinity, and heat output. We also study the temporal and spatial variability in hydrothermal circulation. The two-phase simulation results show that permeability plays an important role in plume structure and heat output of hydrothermal systems, but it has little effect on vent fluid temperature and salinity, given the same bottom temperature. For some permeability values, multiple plumes can vent at the seafloor above the simulated magma chamber. Temporal variability of vent fluid temperature and salinity and the complexity of phase separation suggest that pressure and temperature conditions at the top of the axial magma chamber cannot be easily inferred from vent fluid temperature and salinity alone. Vapor and brine derived fluids can vent at the seafloor simultaneously, even from neighboring locations that are fed by the same plume.