Freshwater cyanobacterial blooms have increased worldwide, channeling organic carbon into these systems, and threatening animal health through the production of cyanotoxins. Both toxic and nontoxic
Microcoleus
proliferations usually occur when there are moderate concentrations of dissolved inorganic nitrogen, but when phosphorus is scarce. In order to understand how
Microcoleus
establishes thick biofilms (or mats) on riverbeds under phosphorus-limiting conditions, we collected
Microcoleus
-dominated biofilms over a 19-day proliferation event for proteogenomics. A single pair of nitrogen-dependent
Microcoleus
species were consistently present in relatively high abundance, although each followed a unique metabolic trajectory. Neither possessed anatoxin gene clusters, and only very low concentrations of anatoxins (~2 µg kg
−1
) were detected, likely originating from rarer
Microcoleus
species also present. Proteome allocations were dominated by photosynthesizing cyanobacteria and diatoms, and data indicate biomass was actively recycled by
Bacteroidetes
and
Myxococcales
.
Microcoleus
likely acquired nutrients throughout the proliferation event by uptake of nitrate, urea, and inorganic and organic phosphorus. Both species also harbored genes that could be used for inorganic phosphate solubilization with pyrroloquinoline quinone cofactors produced by cohabiting
Proteobacteria
. Results indicate that
Microcoleus
are equipped with diverse mechanisms for nitrogen and phosphorus acquisition, enabling them to proliferate and out-compete others in low-phosphorus waters.