Iffy Onoura made a couple of changes to the side that beat Bournemouth with Lee Peacock replacing Rory Fallon, Albert Jarrett replacing Jamie Cureton, and Sean O'Hanlon replacing Charlie Comyn-Platt.
Swindon had a couple of early half chances and had plenty of the ball but coundn't make any of the chances count before Southend opening the scoring on 31 minutes when Luke Guttridge headed in from close range after Southend's first shot had been saved by Rhys Evans.
Then less than a minute after the restart Southend scored a second after a good run from Wayne Gray who passed to Mark Gower who's shot from the edge of the area beat the diving Rhys Evans to make it 2-0 in as many minutes.
At half time Jamie Cureton came on to replace Aaron Brown. Cureton did come close for Swindon later on, but his shot went just wide.
Gurney and Peacock both came close for Swindon in the final couple of minutes which was Swindon's best spell of play but the referee blew up for full time before Swindon had the chance to score.
Overall a fairly average game with neither side having many chances at scoring, just that Southend took their two chances well which is why they are now back at top of the table. The defeat leaves Swindon in 23rd place with one game in hand which is at home to Walsall on Tuesday evening.