Ocean currents, fronts, and eddies shape the distribution of phylogenetic and functional microbial biodiversity, sustaining a mosaic of ecosystem structures with both high and low productivity. Major sampling campaigns have created a wealth of knowledge about the Atlantic microbiome; however, we lack in-depth understanding of how microbial diversity and primary productivity covary at fine spatial scales (~10-100 km). Here, we present results from an Atlantic Ocean transect ( ~50°S - 50°N), sampled at every ~0.5° latitude. We combined in-situ rate measurements of primary productivity, 16S and 18S rRNA gene sequencing, and physicochemical analyses to investigate associations between hydrography and microbial diversity We detected boundaries of ecological regions - partially coincident with Longhurst provinces – with high and low chl a signatures. Eukaryotic autotrophs and prokaryotic heterotrophs showed higher beta diversity in high chl a provinces, while beta diversity of mixotrophs, cyanobacteria and eukaryotic heterotrophs was higher in low chl a provinces. Additionally, we calculated productivity-specific length scales to assess key dimensions of biological-physical coupling across our transect. We observed a link between advection driven by surface currents and patchiness of microbial diversity signals within provinces. Our integrative approach suggests that evaluating trophically disaggregated diversity alongside productivity and advection will improve our understanding of the mosaic nature of microbial provincialism.