The distributions of a variety of variables were used to characterise the physicochemical structure of inner bay waters in a reefal bay with a central channel. The aim was to describe emanations of the bay waters and the effectiveness of particular variables in depicting these emanations. In Wreck Bay—a semienclosed reefal bay located along the Hellshire south-east coast of Jamaica—distribution in temperature, salinity, dissolved oxygen, pH, and specific conductivity were used as potential indicators of the inner bay waters and their emanations. Variable profiles and contours showed that salinity and specific conductivity were found to be unreliable in characterising the bay waters because of the interruptions from numerous submarine seeps found inside and outside of the bay. However, temperature, pH, and dissolved oxygen were more robust in characterising bay waters with continuity from the inner bay, past the reef, and out to sea, even with the presence of the seeps. Surface emanations of bay waters beyond the reef were pronounced with the land-breeze regime but retarded by the entrainment of the sea breeze. Using these variables, it was evident that the reef was not effective in cutting off bay water and that inner bay waters and their characteristics persisted beyond the reef.