In the decade following documented volcanic activity on the East Pacific Rise near 9°50′N, we monitored hydrothermal vent fluid temperature variations in conjunction with approximately yearly vent fluid sampling to better understand the processes and physical conditions that govern the evolution of seafloor hydrothermal systems. The temperature of both diffuse flow (low-temperature) and focused flow (high-temperature) vent fluids decreased significantly within several years of eruptions in 1991 and 1992. After mid-1994, focused flow vents generally exhibited periods of relatively stable, slowly varying temperatures, with occasional high- and low-temperature excursions lasting days to weeks. One such positive temperature excursion was associated with a crustal cracking event. Another with both positive and negative excursions demonstrated a subsurface connection between adjacent focused flow and diffuse flow vents. Diffuse flow vents exhibit much greater temperature variability than adjacent higher-temperature vents. On timescales of a week or less, temperatures at a given position within a diffuse flow field often varied by 5°–10°C, synchronous with near-bottom currents dominated by tidal and inertial forcing. On timescales of a week and longer, diffuse flow temperatures varied slowly and incoherently among different vent fields. At diffuse flow vent sites, the conceptual model of a thermal boundary layer immediately above the seafloor explains many of the temporal and spatial temperature variations observed within a single vent field. The thermal boundary layer is a lens of warm water injected from beneath the seafloor that is mixed and distended by lateral near-bottom currents. The volume of the boundary layer is delineated by the position of mature communities of sessile (e.g., tubeworms) and relatively slow-moving organisms (e.g., mussels). Vertical flow rates of hydrothermal fluids exiting the seafloor at diffuse vents are less than lateral flow rates of near-bottom currents (5–10 cm/s). The presence of a subsurface, shallow reservoir of warm hydrothermal fluids can explain differing temperature behaviors of adjacent diffuse flow and focused flow vents at 9°50′N. Different average temperatures and daily temperature ranges are explained by variable amounts of mixing of hydrothermal fluids with ambient seawater through subsurface conduits that have varying lateral permeability.