A father has lamented the loss of two Yarra footbridge "love locks" dedicated to his young daughters, penning an emotional letter to Melbourne's lord mayor.

Kevin Neville, from Southbank, has written to lord mayor Robert Doyle about the decision to remove thousands of lovingly attached padlocks from the bridge between Southbank and Flinders Street Station.

Mr Neville and his daughters, aged two and three at the time, attached two locks to the bridge in 2013, with the words: "Daddy and I. Together Forever" written on each lock.