Crocker Reef was the site of an integrated reefscape characterization effort focused on calcification and related biogeochemical processes as part of the USGS Coral Reef Ecosystem Study (CREST) project. This effort included two intensive seasonal sampling trips to capture summer (July 8 to 17, 2014) and winter (January 29 to February 5, 2015) conditions. This data release represents water column microbial and environmental data collected for use as metadata in future publications examining reef metabolic processes via metagenomes derived from water samples and fine-scale temporal and spatial carbonate chemistry measurements. Microbial data are total bacterial counts per milliliter seawater, total viral counts per milliliter of seawater, and plate counts using Thiosulfate Citrate Bile Salts Sucrose (TCBS) agar of Vibrio (bacteria) per milliliter of seawater. Environmental data are water temperature, salinity, dissolved oxygen, and pH.