Fortuna said the overflow resulted in a spill of 1,500 cubic metres of water carrying sediment and minor amounts of fine tailings from the facility's drainage system into the nearby Coyote Creek.
The Vancouver-based company said no industrial process water was discharged in the incident, and stressed the San Jose operation used a cyanide-free process to produce concentrate.
The company said it was mitigating the risk of future overflows by immediately increasing its pumping capacity at the contingency pond. No damage was reported to the tailings dam or to the dry stack infrastructure and both remained fully functional.
The company had notified local and federal authorities and was currently working with them as they conducted inspections of its facilities and the Coyote Creek.
The incident stole some of the sheen from the company's September-quarter production results.
Combined output from San Jose and the Caylloma mine, in Peru, came to 2.23 million ounces silver during the period, and reflected a 11% year-on-year increase. Gold output fell 6% to 12,542oz.
Silver and gold output for the first nine months totalled 7Moz and 42,140oz, respectively, 13% and 16% above plan.
Fortuna said it was on schedule to produce 8.3Moz silver and 48,300oz gold, or 11.4Moz silver equivalent in 2018.
The equity fell more than 17% during intraday trading Thursday to hit a new low of C$4.60 a share. It managed, however, to claw back some losses to close down 3.06% at C$5.38 apiece, giving the enterprise a market valuation of $860 million.