Little is known about inorganic fertilizer or manure effects on organic C (OC) and inorganic C (IC) losses from a furrow irrigated field, particularly in the context of other system C gains or losses. In 2003 and 2004, we measured dissolved organic and inorganic C (DOC, DIC) and particulate OC and IC (POC, PIC) concentrations in irrigation inflow, runoff, and percolation waters (six to seven irrigations per year); C inputs from soil amendments and crop biomass; harvested C; and gaseous C emissions from field plots cropped to silage corn (Zea mays L.) in southern Idaho. Annual treatments included: manure treatment (M) 13 (Year 1) and 34 (Year 2) Mg ha-1 stockpiled dairy manure; inorganic fertilizer treatment (F) 78 (Year 1) and 195 (Year 2) kg N ha-1 inorganic N fertilizer; or no amendment treatment (NA) as a control. The mean annual total C input was 15.7, 10.8, and 10.4 Mg ha-1 for M, F, and NA, respectively, while total C outputs for the three treatments were similar, averaging 12.2 Mg ha-1. Manure plots ended each growing season with a mean net gain of 3.3 Mg C ha-1 (a positive net C flux) vs. a net loss for F and NA (-1.6 and -1.5 Mg C ha-1, respectively). The C added to M was ?1.5 × that added to F or NA, yet relative to F, M increased gaseous C emissions only 1.18×, increased runoff DOC losses only 1.04×, decreased particulate runoff total C 19%, and decreased percolate DOC 32%. Increased C gas emissions from manure (relative to fertilizer) were less when silage was removed than when retained (1.18× vs. 2× reported in other studies). This suggests a means by which manure applications to corn crops can be managed to minimize C emissions. Amendments had both direct and indirect influences on individual C components, e.g., the losses of DIC and POC in runoff and DOC in percolation water, producing temporally complex outcomes, which may depend on environmental conditions external to the field. © Soil Science Society of America.