Between 2019 and 2020, the Gambier lagoon was instrumented over a period of 9 months with a large array of autonomous oceanographic instruments measuring temperature, pressure, and current. Two deployments were conducted from June to October 2019 (Leg1) and from late October 2019 to late February 2020 (Leg2). A total of 16 instrumented locations were spread across the lagoon and on the forereef. Physical parameters were measured to characterize the wave climate, tide and surges, lagoonal circulation, and spatial and vertical temperature variabilities. Those observations were part of the ANR-funded MANA project (2017–2022) and its derivatives that were aimed at improving knowledge of processes influencing the spat collection of Pinctada margaritifera oysters that are used for black pearl farming and production. This dataset was a prerequisite for the development of a high-resolution biophysical model on the Gambier lagoon that is aimed at understanding the connectivity of oyster larvae (Bruyère et al., 2023a). The sampling strategy focused on the northern region of the Gambier lagoon and especially on the sub-lagoon of Rikitea, which is a prime spat collection site. The dataset was post processed, quality controlled, and is archived in a dedicated repository with a permanent DOI via the SEANOE marine data platform (https://doi.org/10.17882/94148, Andréfouët et al., 2023b).