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Abstract Freshwater wetlands process large amounts of nutrients originating from agricultural fields. Yet, these systems also have the potential to produce substantial amounts of nitrous oxide (N₂O) and methane (CH₄), both potent greenhouse gasses (GHGs). Agricultural land use alters delivery of nutrients and carbon (C) to downstream wetlands, and changing climate is altering hydroperiods. These drivers modulate wetland microbial processes responsible for GHG production including denitrification and methanogenesis. Studies have correlated GHGs to C quantity and nutrients independently; fewer studies identify how nutrients and C composition interact to modulate GHG concentrations in wetlands. In wetlands located in Indiana, USA, we studied how CH₄, N₂O, and carbon dioxide (CO₂) correlated to C quantity and composition, nutrient concentrations, size, hydrology, and surrounding agricultural land use. CH₄production was correlated to dissolved organic carbon (DOC) concentrations and composition using UV‐Vis spectroscopy. CH₄concentrations were positively correlated to spectral slope from 275 to 295 nm, an indicator of autochthonous primary production, and negatively correlated to humification index. N₂O concentrations positively correlated to total dissolved nitrogen and humification index (HIX). CH₄concentrations were highest in the large wetland with negligible canopy cover, dense macrophytes and algae, and high concentrations of autochthonous‐like DOC. Thus, we suspect phototrophic methanogenesis is an important driver of CH₄variation across systems. Concentrations of N₂O were highest in the agricultural wetland, likely driven by higher NO₃⁻concentrations. Our findings suggest agricultural nutrients strongly shift greenhouse gas production profiles but do not necessarily increase global warming potential of GHGs released by wetlands.