Microbes including phytoplankton are the foundation of ocean, coastal and freshwater ecosystems. Up until recently, investigations of microbial diversity and abundance in marine and aquatic realms were largely compromised because researchers had to bring fixed and cryopreserved samples from natural habitats in field locations back to land based laboratories. With funding support from the Australian Research Council and partner institutions, we established a purpose-built, transportable, live cell analysis laboratory (the Micro-CSI) which houses a BD Influx cell sorter as well as a high-content imaging system (GE IN Cell Analyzer 2200). The laboratory is the first of its kind in Australia and since 2015 has been utilized in three oceanic research voyages on Australia’s blue water research vessel, Investigator. The Micro-CSI has analyzed hundreds of live samples, and sorted dozens of phytoplankton isolates from the southwestern Pacific Ocean. Here we share some experiences and lessons learned from its operation, and discuss its research potential and future use.