Knowledge is lacking for sediment organic matter degradation and its influence on water quality for low gradient agriculturally impacted streams despite their importance for freshwater biogeochemical cycles and ecological restoration. We hypothesized degradation rates vary across sediment type and are a function of the connectivity regimes for low gradient systems. We carried out aerobic incubation experiments to assess oxidation and mineralization-nitrification rates and changes in stable isotopic ratios for sediment and dissolved organic matter and nitrate. Sediment originated from erosion across the watershed’s surface shows higher carbon oxidation rates (k = 3.9x10-3 d-1) and lower nitrogen mineralization-nitrification rates (k = 7.9x10-4 d-1) compared to sediment originated from the creek’s streambed that integrates algae and other autotrophic matter (k = 1.6x10-3 d-1 and k = 3.4x10-3 d-1). Differences are attributed to sediment transport of humified and plant matter during storms of high watershed connectivity and sediment transport of autochthonous sediment for low connectivity. Results support our hypothesis and suggest that the sediment connectivity regime of the watershed exhibits control on biogeochemical cycling of the stream network. Cumulatively, sediment degradation rates were one to two orders magnitude higher than previously assumed. Sediment rates reflect aerobic waters and place the organic matter as active and comparable to reported turnover of algae and fine sized leaf litter. Stable isotopic ratios of sediment change marginally for the two sediment types for carbon (ε = 0.4‰ and 1.3‰) and nitrogen (ε = 3.5‰ and 1.5‰). Dissolved organic nitrogen of stream water degraded similarly across all experiments (k = 1.8x10-2 d-1), and turnover rates were an order of magnitude higher than recent rates reported for lake water. Nitrate concentration in the solute increased by an average 35% during experiments and the nitrogen stable isotopic ratio of nitrate decreased by over 1‰ showing the potential of sediment and dissolved organic matter degradation to influence nitrate flux and its isotopic signal.