Cold seeps, hydrothermal vents, deep water coral reefs, and submarine canyon systems are hotspot habitats characterized by intermediate to high fluid advection. They are shaped by a complex interplay of physical, biological, geochemical, and geological processes. Biogeochemical and physicochemical gradients in these ecosystems are frequently extremely steep and temporally and spatially variable. Zones of elevated microbial activity, such as the methane-sulfate interface at cold-seep sites, usually encompass no more than a few millimeters. Recovery of samples for further shipboard analysis from such hotspot zones generally causes severe artifacts in the biogeochemical gradients. Hence, to quantify chemical gradients, microbial processes, and transport rates in deep-sea hotspot ecosystems, we have developed and operated a variety of specialized in situ instruments (Figure 1).