Nonperennial streams make up 80% of stream miles in Kansas, yet we still struggle to predict how drying and rewetting shapes biogeochemical processing. Hydrologic variation alters sediment redox conditions, organic matter quantity and quality, and shifts microbial community compositions. Most of our understanding of biogeochemical processes comes from perennially flowing systems. The studies that consider nonperennial streams do so when surface water is present, leaving a gap in how drying regulates biogeochemical processes. To address this, we performed monthly samplings and incubations across three watersheds. We used high-frequency water presence/absence data to characterize two network-scale and four local-scale drying metrics. We utilized structural equation modeling to understand the effects of drying on organic matter content and microbial N processes. Biogeochemical responses were driven more by site-level drying history than by network-scale connectivity. Dry sites accumulated more sediment organic matter, and metrics of local drying strongly predicted organic matter content (β = 0.45). Organic matter enhanced both DEA (β = 0.45) and nitrification (β = 0.18), but long dry durations suppressed the positive effect of organic matter on DEA (β = -0.21) (slope = 0.66 with low drying frequency and slope = 0.24 with high drying frequency). Nitrification increased with longer wet durations (β = 0.28), but intense wet-up events reversed the stimulatory effect of organic matter (β = -0.30). Simple-slope analysis showed that organic matter content stimulated nitrification under network-scale contraction conditions (slope = 0.48) and became slightly negative during network-scale wet up (slope = –0.12). NO₃⁻ concentrations decreased with increasing frequency of drying and increased with increasing nitrification potential. NH₄⁺ concentrations increased with more frequent drying and decreased with DEA. While drying promotes the accumulation of organic matter in sediment, thus promoting NO₃⁻ removal through denitrification, it also suppresses nitrification and promotes the accumulation of NH₄⁺. Increasing NH₄⁺ concentrations can result in nutrient pollution, harmful algal blooms, and oxygen depletion. With the ubiquity of nonperennial streams increasing in Kansas and globally, understanding the impacts of drying frequency and duration on N removal processes is imperative to inform sustainable management practices.