Rates of nutrient cycling processes, as well as the drivers and mechanisms of variation in those rates, may change at different time scales. Although seasonal patterns in these process rates have been studied, it's unclear how they may respond to shifting seasonal dynamics (i.e., earlier snowmelt and extreme weather events), and we know little about how rates may vary at shorter daily and weekly timescales. Understanding this variation across temporal scales is essential to understand how nutrient cycling processes operate in aquatic ecosystems and predict how they may respond to global change. This study quantified denitrification and nitrogen (N) fixation rates seasonally and daily in a northern temperate river, and explored how environmental conditions such as discharge, light, and nutrients were related to that variation at different time scales in the Pilgrim River, tributary of Lake Superior located in the Upper Peninsula of Michigan, USA. This dataset includes denitrification and nitrogen fixation rates measured from May 2017- May 2019 on rock and sediment substrates as well as physical and chemical properties of the river measured during each sampling event.