The composition, transformation, and transport of dissolved inorganic nitrogen (DIN) was compared in waters associated with two lowland streams in Costa Rica. The Salto River is enriched by geothermal-based soluble reactive phosphorus (SRP), which raises the concentration up to 200 μg/L whereas Pantano Creek, an unimpacted tributary, has an SRP concentration <10 μg/L. Ammonium concentration in springs adjacent to the Salto and Pantano was typically greater than channel water (13 of 22 locations) whereas nitrate concentration was less (20 of 22 locations). Ground waters were typically high in ammonium relative to nitrate whereas channel waters were high in nitrate relative to ammonium. Sediment slurry studies indicated nitrification potential in two sediment types, firm clay (3.34 μg N∙cm−3∙d−1) and uncompacted organic-rich sediment (1.76 μg N∙cm−3∙d−1). Ammonium and nitrate amendments to each stream separately resulted in nitrate concentrations in excess of that expected after correction for dilution using a conservative tracer. SRP concentration was not affected by DIN amendment to either stream. SRP concentration in the Pantano appeared to be regulated by abiotic sediment exchange reactions whereas DIN composition and concentration were regulated by a combination of biotic and abiotic processes.