The first chance fell to Harwich striker Joe Knight but he could not get the clean connection that he wanted and his shot went outside the post.
From the next Shrimpers attack Liam White, making his 100th appearance for the club, fired in a 30-yard shot which was well saved by the home goalkeeper.
White Ensign were to prove strong opposition and Harwich goalkeeper Brad Cook did well to punch away under pressure and then when the ball came back at him when he was off his line, he pulled off an excellent block.
Harwich were producing some good moves and from White's pass Tyler Sullivan powered a shot over the crossbar, then full-back Tiwa Odufuye made a quick run before finishing with a clever lob that went inches wide of the goal frame.
With 30 minutes gone, Knight hit a low shot that was heading for the net but the White Ensign keeper excelled with a super diving save.
With half time approaching, White Ensign had their best opportunity but could not find the net with a shot that went the wrong side of the post.
In the 54th minute, White Ensign took the lead when their dangerous number nine, Riley Weir, got goal side of the Harwich defence and netted with a well-taken shot.
Harwich were undeterred, with White outstanding in midfield, his tackling and distribution first class.
The Shrimpers' reward came midway through the second half when, from just outside the penalty area, Knight pounced to equalise with a trade-mark snap shot that went low into the corner of the net.
The visitors' tails were up with White working a shooting opportunity for himself that went inches wide and Alfie Canning creating a chance from which Sullivan's drive went also just outside the post.
Fifteen minutes remained when Harwich took the lead. Louie Bloom (pictured) had worked back and forth tirelessly and from 25 yards he placed his shot low into the corner of the net.
For White Ensign, the crafty Weir, operating on the wing and ghosting into the centre, eluded the defence and Cook was called upon to make another fine save to thwart him.
For Harwich, central defender Charlie Canham had been dominant throughout, well supported by skipper Jack Wood.
In the final minutes, Harwich almost scored a third goal when substitute Zac Pedro's shot struck the upright.
The heavy, rain-sodden Great Wakering pitch was testing the stamina of both teams and it was a match in which the entire Harwich team deserved top marks.
Harwich team: Brad Cook, Tom Watkins, Charlie Canham, Jack Wood (captain), Tiwa Odufuye, Tyler Sullivan, Liam White, Alfie Canning, Louie Bloom, Jamie Eveleigh and Joe Knight. Substitutes: Zac Pedro, Cody Harrison, Reuben Keeys (all used) and Jeremiah Ajisafe (not used).