Chase Numata knocked in his first two runs as a Thresher, but Clearwater could not overcome a five-run Manatees outburst in the fifth in dropping the series finale, 8-4 at Space Coast Stadium.
Emmanuel Marrero also collected his first hit and RBI as a Thresher, plating the game's first run on a single that scored Willians Astudillo in the second inning.
Brevard County (17-22) pulled even in the fourth against Victor Arano (0-5). Clint Coulter and Garrett Cooper each doubled to knot the game up at one.
The Threshers (19-21) rallied to bounce back ahead an inning later.
With two outs, JP Crawford and Andrew Pullin teamed up for back-to-back singles. Numata put the Threshers in front by sending a two-bagger to center to plate both Crawford and Pullin, making it a 3-1 game.
In the bottom of the fifth, the Manatees rallied to go ahead for good.
The Threshers were charged with three errors in the inning, as Brevard County pushed across five runs on four hits.
Arano would ultimately permit five runs - four earned - on six hits across his 4.1 innings in the loss.
Clearwater's final tally came in the seventh, after Crawford singled and went to third on a two-base error by Garcia in center. Pullin brought him down the line on a grounder to short, cutting the deficit to 7-4.
The Threshers took two-of-three from Brevard County, and continue a seven-game road swing on Thursday as they head to Palm Beach to open a four-game set against the Cardinals. First pitch will be at 6:35 p.m., as Mark Leiter, Jr. (2-0) toes the rubber opposite Will Anderson (1-1).