The Mariana forearc system, in the northwestern Pacific, is known as the only convergent margin setting with currently active serpentine mud volcanism. The Fantangisña serpentinite mud volcano lies 62 km west of the Mariana trench, within the influence of the North Equatorial Current (NEC). Cores recovered by International Ocean Discovery Program (IODP) Expedition 366 contain pelagic sediments overlying layered serpentinite mud deposits. At the bottom of the sequence, nannofossil‐rich forearc deposits were recovered from under the seamount edifice. In this study, we investigated 47 samples from Site U1498A on the southern flank of the seamount for benthic and planktonic foraminifera assemblages. Statistical analyses on planktonic assemblages differentiated two sample groups related to the ratio between thermocline/mixed layer taxa, which indicate fluctuations in the depth of the thermocline (DOT) during the Pleistocene. Variations in the DOT reflect changes in the intensity of the NEC associated with El Niño/La Niña conditions. Mudflows do not influence the ecology of planktonic foraminifera but possibly enhance their preservation against dissolution, which was instead detected in the pelagic deposit as suggested by common Globigerinoides conglobatus. Benthic foraminifers were rare in serpentinite mud deposits as they are severely affected by mudflows. Conversely, they showed high diversity pre‐/post‐mud‐volcanism, and indicate oligotrophic bottom‐water conditions.