On April 5, 2016, Rivera signed a minor league deal with the New York Mets. He was called up to the major league team on April 26, 2016, when Travis d'Arnaud was placed on the disabled list. He started for the Mets in their Wild Card game against the San Francisco Giants, going 1 for 3 and throwing out Denard Span. Throughout the season he was Noah Syndergaard and Seth Lugo's personal catcher. On December 3, 2016, Rivera and the Mets avoided salary arbitration by agreeing to a one-year, $1.75 million contract.