Jackson Estuarine Laboratory maintains a well equipped laboratory as well as a fleet of small estuarine research vessels. The building and adjoining greenhouse has full seawater capabilities on a year round basis. Mesocosms are maintained outside during the summer season. Within the laboratory JEL has a full analytical laboratory (nutrient autoanalyzer, gas chormatographic elemental autoanalyzer, liquid scintillation counter, spectrophotometer, and image analysis system), sedimentology and benthic laboratory (grain size, organic content and infaunal identification equipment) and microbiology laboratory equipped for ribotyping, community analysis, PCR, gene probes and traditional culture techniques (chemiluminescence imaging system, thermocycler, gel electrophoresis, liquid scintillation counter, epifluorescence microscope, centrifuges, incubators, ovens).
Boating facilities at JEL include a causeway with a 2,000 pound capacity crane and a floating dock with slip spaces for four boats. There is also a tide-restricted boat ramp on the adjacent NH Fish and Game Department property. Boats available at JEL include five outboard-powered vessels ranging from a 12-foot skiff to a 22-foot center-console, and a 24-foot diesel-powered inboard.
The main building also houses a library containing holdings relevant to coastal and estuarine research as well as the JEL Contribution Series of faculty publications and the JEL Report Series of unpublished documents.