AER regulates coal mining in respect of the Coal Conservation Act, which is primarily with respect to responsible/efficient coal resource recovery. An environmental approval under EPEA must still be obtained. For this mine (and any open pit mine over 45,000 tonnes/year production), it is mandatory that a provincial environmental impact assessment under EPEA be conducted. The project will also have to be assessed under the federal Impact Assessment Act. All these regulatory agencies (AB Environment, AER, federal Impact Assessment Agency) coordinate to ensure no overlap. In the past when both federal and provincial assessments are called for (as would be the case here), a joint review panel has often been struck with one of the agencies leading the review on behalf of the others. Not sure how it will work now under the new federal IAA, as there haven't really been any projects put forth subject to that yet, but will probably be in line with this historical joint review process.
Bottom line is that a proposal like this will be subject to a full environmental impact assessment with both federal and provincial agencies involved. An EIA involves, from the getgo, stakeholder consultation and input as to the terms of reference for the EIA/joint review panel. That would be the ideal time to ensure that fisheries related matters are prominent and baked into the terms of reference for the EIA.