It was the Mariners' first derby win in eight games under manager Russell Slade and the match was over as a contest by the 43rd minute when Grimsby scored the third goal.
On a tricky pitch that survived the inspections it was proved to be a correct decision by West Midlands referee Ray Olivier to play the match.
Grimsby adapted better to the conditions and took the points with some ruthless finishing. When the home side took their feet off the pedal in the second half Lincoln had one or two half chances but never seriously threatened to get back into it.
Grimsby opened the scoring on eight minutes through midfielder Ciaran Toner who scored in the same fixture last season for Lincoln.
It was Toner's first goal for Grimsby and was a sweet strike just inside the box after a great pull-back by striker Michael Reddy.
Reddy scored the second on 24 minutes after being played clear by striking partner Gary Jones.
Grimsby were denied a third goal on 42 minutes when keeper Alan Marriott tipped a Rob Jones header onto the bar. But from the resulting corner the ball came out to winger Andy Parkinson who cracked home a beauty from 30 yards.
There was no way back for Lincoln and manager Keith Alexander replaced striker Derek Asamoah with fellow striker Marvin Robinson for the second period.
And it was Robinson who had two reasonable second half chances, but neither extended Grimsby keeper Steve Mildenhall, whose only save of the night came from defender Gary Croft who nearly headed into his own goal from a corner before Grimsby scored.
Not only does the result take Grimsby top of the table but it takes their holiday points haul to six from six.