We monitored salinity and temperature in pools at different elevations in two marshes on the Bay of Fundy to assess variability in pool environments and how climate change might affect these ecosystems. Water temperatures reached a maximum of 36.1°C, and ice covered pools in the winter. Ice lifting out of ponds in the spring scoured bottoms. Salinity ranged from 4 to 41. Environmental variability was mainly driven by weather. Variability in pool temperature declined with decreasing elevation. Regular tidal flooding at lower elevations moderated both temperatures and salinity. Variability in pool salinity was greatest in the middle marsh region, since proximity to groundwater also moderated salinity at high elevations. Projections of milder winters should reduce formation of ice in pools, resulting in decreased scour, and possibly shallowing of pools. This, accompanied by projected increases in extreme weather, will increase salinity variability, thus increasing stress to organisms in an already stressful environment.