In summer 2011, the two Russian MIR submersibles were brought to Switzerland to perform deep water dives in Lake Geneva. Research teams from several environmental science institutes, both national and international, participated in this interdisciplinary effort to investigate the deeper parts of Lake Geneva. Using the MIRs allowed the scientists to see and precisely select the sites where they could extract specific sediment cores and carry out detailed in situ measurements at the sediment–water boundary. One focus site was the surrounding of the outlet of the wastewater treatment plant of the City of Lausanne, which discharges into the Vidy Bay. The investigations concentrated on the pollution of the local sediments, pollution-related ecotoxicological risks, microbial activity and spreading and removal of the effluents from the bay to the open waters of the lake. The other focus site was the Rhône River delta and its subaquatic canyons, which formed as a result of the long-term interplay of the deposition of river-borne sediments and flood-triggered canyon erosion events.