Cowan, 25, was signed from Canvey Island in March 2005 but has found first-team action hard to come by this season and has had his contract cancelled.
"We've had contact from Grays and we've agreed to cancel his contract and let him go," Shrews boss Gary Peters confirmed.
"He's got enough ability to go on and do well, he's a footballing centre-half and that is probably the reason he hasn't played much for us.
"This season he's played a few games and started to get the hang of our division and had I not had as many centre-backs he would have played more games."
Harding, 22, arrives on loan until the end of the season from the MK Dons, having finished his loan spell with The Shots this week.
He has made over 50 appearances for the Dons but has failed to break into the first team picture this season under the management of Martin Allen.
20-year-old Fernandez has joined on a month's loan and has already had loan spells with Wycombe and Blackpool this season.