Brookfield Gardens faces three counts under the province's Environmental Protection Act's watercourse and wetland protection regulations.
The provincial government has said about 1,150 brook trout, speckleback, rainbow trout and Atlantic salmon were found dead.
The dead fish were reported Aug. 9 as they started to appear over a 3.8-kilometre stretch of the North River in central P.E.I.
The government says the charges against Brookfield Gardens relate to the cultivation of an agricultural crop in the North Milton area.
The company, which grows and sells vegetables to grocery stores and wholesalers, is due in Charlottetown provincial court Nov. 24.
The charges include cultivating an agricultural crop within 15 metres of a watercourse boundary or wetland boundary, altering or disturbing the ground or soil within 15 metres of a watercourse boundary or wetland boundary without a licence or permit, and cultivating one or more hectares of row crop on a parcel of land with a slope greater than nine per cent without a management plan.