In the semi-arid Texas High Plains, agricultural systems which integrate cattle with perennial-based systems have been shown to conserve water, maintain productivity and increase soil organic matter.  Offsets to enhanced C sequestration however can occur via nitrous oxide (N₂O) and carbon dioxide (CO₂) emissions.  The purpose of this study is to examine the magnitude and seasonal patterns of CO₂ and N₂O fluxes associated with two long-term (>5 years) ICLs supporting five vegetation types.  ICL_1, a dryland system, was comprised of three vegetation types: cotton and millet (planted in rotation) and perennial native grasses (PNG).  ICL_2, a deficit-irrigated system, was comprised of bermudagrass and W.W.B.Dahl-Old World Bluestem (OWB).  Fluxes (CO₂ via Li-COR LI-8100 system; N₂O via static chambers) were measured weekly from July-September 2010 and monthly from October-June 2011.  Fluxes of CO₂ and N₂O averaged 113 mg CO₂-C m^-2h^-1 and 0.006 mg N₂O-N m^-2h^-1, respectively and most responsive following precipitation events.  Greatest fluxes were measured under bermudagrass, followed by PNG and OWB, with the lowest fluxes produced in cotton-millet rotations.  Peak bermudagrass CO₂ flux (508 mg CO₂-C m^-2h^-1) occurred on 1-July-2010.  N₂O fluxes produced only two significant spikes occurring within 48-hours of precipitation events (0.059 mg N₂O-N m^-2h^-1 on 30-June-2010 and 0.113 mg N₂O-N m^-2h^-1 6-August-2010).  From December to April 2011 CO₂ fluxes averaged 37 mg CO₂-C m^-2h^-1 during the dormant period for all vegetation types.  Increased N₂O fluxes were observed in ICL_1 following the largest precipitation event (128.5 mm) of the active phase compared to ICL_2 in which flux rates decreased.   As of mid-August 2010 N₂O fluxes in both ICLs had decreased to an average 0.005 mg N₂O-N m^-2h^-1 with no significant variations detected.  Although bermudagrass produced the greatest CO2 and N2O fluxes, they are low compared to most cropland emissions, and are partially offset by higher total C contents.