Fish habitat loss has been prevalent over the last century in Canada. To prevent further erosion of the resource base and ensure sustainable development, Fisheries and Oceans Canada enacted the habitat provisions of the Fisheries Act in 1976. In 1986, this was articulated by a policy that a "harmful alteration, disruption, or destruction to fish habitat" (HADD) cannot occur unless authorised with legally binding compensatory habitat to offset the HADD. Despite Canada's progressive conservation policies, the effectiveness of compensation habitat in replicating ecosystem function has never been tested on a national scale. The effectiveness of habitat compensation projects in achieving no net loss of habitat productivity (NNL) was evaluated at 16 sites across Canada. Periphyton biomass, invertebrate density, fish biomass, and riparian vegetation density were used as indicators of habitat productivity. Approximately 63% of projects resulted in net losses in habitat productivity. These projects were characterised by mean compensation ratios (area gain:area loss) of 0.7:1. Twenty-five percent of projects achieved NNL and 12% of projects achieved a net gain in habitat productivity. These projects were characterised by mean ratios of 1.1:1 and 4.8:1, respectively. We demonstrated that artificially increasing ratios to 2:1 was not sufficient to achieve NNL for all projects. The ability to replicate ecosystem function is clearly limited. Improvements in both compensation science and institutional approaches are recommended to achieve Canada's conservation goal.