The Liberal government changed the endangered species regulation in 2013 to exempt some industries such as forestry, oil and gas, and mining from a prohibition against harming at-risk species or destroying their habitats.
The exemptions remove the law's core protections for almost all of Ontario's 155 endangered and threatened species, Ontario Nature and Wildlands League argued in Divisional Court.
"In aim and effect, the regulation is contrary to the ESA's purposes — to protect and recover Ontario's most imperilled species," they say in written arguments.
The minister of natural resources failed to determine if the regulation was likely to adversely affect each endangered species, instead he only specifically assessed five species, the groups argue. The minister is required to examine whether a regulation will affect each species, not a few, they say.
"It is impossible to discern, on the face of the minister's determination, whether any significant adverse effects of the regulation were ever identified for individual species, what the nature and extent of any such effects might be, and if those effects were considered to be likely," the groups argue.
"The minister's determination fails to assess the impacts of proposed exemptions on each listed species affected by them without justification, transparency or intelligibility as to why each species was not assessed. That failure cannot fall within a range of possible, acceptable outcomes that are defensible here."
Lawyers for the government argue that the minister duly made that determination and that exemptions can only apply when a proponent meets a number of onerous conditions.
"In order to qualify under one of the regulatory exemptions from the ESA prohibitions, the amendments to the regulation require a proponent to engage in a number of activities intended to minimize adverse effects on endangered and threatened species, mitigate any effects on the species, and in some cases, benefit the species," the government says in written arguments.
"As such, the amendments to the regulation are consistent with the purposes of the ESA."
The government argues that the legislation balances the central concern of protecting at-risk species with social, economic, health and cultural considerations.
"We have to use the best evidence to make our decisions around protecting endangered species," Premier Kathleen Wynne said Wednesday.
"At the same time we have to recognize there are businesses and the agricultural community that is dependent on being able to develop certain land and to manufacture goods...My guess is that over time we will continue to modify and refine that legislation but those changes that we made were very much an attempt to find that balance."