This study presents a methodology for combining archival data storage tags (DSTs) and ultrasonic transmitters to investigate the microhabitat conditions of adult Cancer magister (Dana), inhabiting an estuary. The temperature, salinity and depth experienced by free-ranging Dungeness crabs were recorded at 10-min intervals for periods ranging from 1 week to 8 months. Crabs were tracked using a hydrophone, and tags were recovered via concentrated trapping or returned by recreational fishers for a reward. These methods led to a return rate of 50%. Representative CTD tag data showed that the conditions recorded at fixed stations within the estuary were not reflective of those experienced by free-ranging crabs, but rather crabs were able to orientate and avoid low salinity within the estuary. The prevalence of low salinity exposure was linked to times of increased food availability within the estuary, suggesting that crabs were entering the shallows of the estuary to forage. The techniques used in this study demonstrate that DSTs are a viable means of determining the microhabitat conditions of crustaceans inhabiting highly variable environments.