The interplays between water, air, rock, and life on Earth are key to making our planet habitable. The compositions of the oceans and the atmosphere are set by these interactions, in which microorganisms play a particularly important role. They take CO2 out of the atmosphere by making limestone and organic matter, but they require nutrients like calcium, phosphate, and iron supplied by geological processes to do so. In turn, microbial activity affects the rates and processes by which these nutrients are supplied and cycled. We examine varied compartments of this complex reaction network from vents and seeps in the deep-sea to marine sediments to coral reefs. The Earth holds rich archives that we read using isotopic tracers to understand how element cycling may have varied in the past.