The Habitat Stewardship Program (HSP) is a major pillar in Canada’s National Strategy for the Protection of Species at Risk that supports projects assisting the recovery of species at risk (SAR). To assess long-term and biological outcomes and evaluate taxonomic and geographic coverage of HSP-funded projects using Ontario as a case study, 95 HSP-funded projects for aquatic SAR (2006-2017), were evaluated. Fifteen million CAD was allocated to 66 habitat stewardship projects targeting aquatic SAR. Twenty-nine fish and mussel SAR were targeted in 12 watersheds located primarily in southwestern Ontario. Greater funding was allocated to multi-year projects targeting higher numbers of SAR. Future funding should target geographically widespread SAR and SAR-rich watersheds in southwestern Ontario. To align stewardship actions with aquatic SAR recovery priorities, proposals and reports must identify the threats being addressed by stewardship actions. Standardized pre- and post-activity monitoring should be required to ensure measurable conservation benefits and to enable assessment of the effectiveness of habitat stewardship actions. Similar analyses should be undertaken in other Canadian provinces and territories to evaluate the HSP nationwide.