A large variety of biotic and abiotic processes take place close to the sediment-water interface, causing and being affected by physical, biological and chemical gradients below and above this transition zone. Adequate sampling of this environment is essential for a comprehensive understanding of the complex sea floor ecological systems. The multi-horizon bottom water sampler (BoWaSnapper) presented here was developed for instantaneous sampling of the transition zone above the seafloor and can be deployed in all types of water bodies from coastal seas to full ocean depth (6000 m). The intention was to construct an instrument that could bridge the gap between the sampling of the bottom water column by conventional CTD rosette and sediment sampling gear such as a multiple corer. The BoWaSnapper was designed to be operated on any research ship's wire and allows time-efficient high-resolution sampling of bottom water. The bottommost 2 m are sampled with six vertically adjustable bottles. Prior to closure, the bottles are aligned with the bottom current by means of a vane and flushed by bottom water for several minutes. This ensures that particles dispersed upon the touch-down of the BoWaSnapper are flushed away. An electronic mechanism, activated by a bottom switch, initiates bottle closure after a delay pre-selected by the user. As illustrated by several examples, the transparent bottles (6 L volume each) allow the determination of particle concentrations as well as the analysis of solutes such as nutrients, dissolved gases, and natural radiotracers. Although the sampler is universally suitable for seafloor environments, its special domain is characterised by steep geochemical gradients such as cold vents and submarine groundwater discharge. © 2005 Elsevier B.V. All rights reserved.