Lake Rotoiti formed 11 850–20 000 years ago when lava flows dammed the drainage system through the Okataina caldera, one of the major rhyolitic centres of the intracontinental, back-arc, Taupo Volcanic Zone of North Island, New Zealand. The lake morphology reflects this complex origin, with remnants of the old caldera rim, the lava dam and relict river system being preserved. High resolution seismic reflection profiles (7 kHz) show the drowned river system channelled inflowing water into the lake basin, scouring and depositing sediments and maintaining an active sublacustrine channel in the former river valley. Airfall tephras are preserved in lake sediments. The tephrachronology, established from the surrounding catchments, can be correlated with the siesmic stratigraphy for eight major eruptions over the last 11 850 years. Hydrothermal fields underlying the lake generate gaseous sediments which mask seismic penetration. This is indistinguishable from seismic masking caused by biogenic gas accumulation within the sediments. Venting of hydrothermal gases at the surface creates pockmarks. From the seismic stratigraphy beneath pockmarks seven stages of pockmark genesis have been identified which show pockmarks grow, decay, migrate and persist over several thousand years.