The railways and growing industries began altering Toronto’s waterfront on a large scale in the mid-nineteenth century, 40 to 50 years after the founding of the Town of York (Toronto). Garrison Creek, at the entrance to the harbour west of the early town, and Taddle Creek, which emptied into the bay at the east edge of the town site, both flowed through ravines that were influential in shaping the early layout and growth of the city. The lower reaches of both attracted significant industrial development. In this paper we discuss the archaeological remains of two mid-nineteenth-century sites, a small lime works and an extensive railway repair yard, that represent contrasting adaptations to their surrounding landscape and contextualize these industrial operations in terms of the wider transformation of the waterfront that would ultimately erase all traces of both the sites and the two watercourses on which they were established.